Progress 03/01/13 to 02/28/18
Outputs
Progress Report Objectives (from AD-416): The long-term objective of this plan is to develop sorghum inbred lines that possess superior tolerance to abiotic stresses, and high biomass and grain yield potential. We will integrate natural variation, induced mutation, phenotype-based and marker-assisted selection to identify the desirable traits and introduce them into elite sorghum inbred lines. Specifically, during the next 5 years we will focus on the following objectives: Objective 1: Develop new screening tools and genetic resources to identify sorghum lines with high grain or biomass yield potential under drought and temperature stresses. Subobjective 1A: Evaluate the relationship between dhurrin concentrations and the staygreen trait. Subobjective 1B: Evaluate the diversity of the stay-green trait among sorghum germplasm collections. Subobjective 1C: Evaluate the efficacy of stay-green markers in F1 hybrids. Objective 2: Identify novel sources of genetic variation for cold temperature and drought tolerance in sorghum. Subobjective 2A: Develop high resolution genetic and QTL maps using new ARS mapping populations to discover robust and effective DNA markers conditioning early season cold tolerance, and validate marker-assisted selection using a subset of cold tolerant inbreds. Subobjective 2B: Identify markers or genes associated with high seed number and erect leaf traits. Objective 3: Develop improved grain sorghum and non-grain, energy sorghum breeding lines with high grain or biomass yield potential under high abiotic stress environments. Subobjective 3A: Develop and release novel ARS germplasm with enhanced abiotic stress traits such as stay-green, cold tolerance, high grain number, and erect leaf traits. Objective 4: Accelerate sorghum community trait analysis and trait development, via a new USDA public sorghum crop genome database system, by providing open access to sorghum genome sequence information, germplasm diversity information, trait mapping information, and phenotype information, with an initial emphasis on sugarcane aphid resistance. [NP301, C4, PS4A, C1, PS1A, C2, PS2A, C3, PS3A] Approach (from AD-416): Superior traits that enhance sorghum grain and biomass yield and abiotic stress tolerance, identified previously from mutation population and natural germplasm collections, will be mapped using classical genetic analysis and the state-of- art Next-Generation Sequencing technology. Molecular markers will be developed for the rapid introgression of these traits into elite commercial lines. Lines with high yield potential and superior resilience to abiotic stresses will be developed through a systematic approach integrating physiology, marker-assisted selection, and conventional breeding. This project will provide much needed support for sorghum genomic and genetic research and germplasm improvement. Sorghum is an important feed, biofuel, and food crop in the United States. It is a superior heat and drought resistant crop, and thus its importance for U.S. agriculture is increasing given the impacts of global warming and water scarcity. However, production losses caused by increasing pressure from the sugarcane aphid pest have recently slowed the growth of sorghum production. Thus, increased support for sorghum genomic, genetic, and germplasm information generation and sharing is urgently needed to accelerate the rate of improvement in high-value target traits. To meet this critical need, a new USDA-ARS public sorghum genomics and genetics database will be developed to increase information management capacity, promote open access data and information sharing, and open access to data analysis tools; to facilitate the development and implementation of standardized methods for the collection, analysis, and utilization of new sorghum data; and to enable sorghum researchers and breeders to accelerate the development of superior performing cultivars for U.S. producers. The project will leverage strategic biology-enabled information at USDA-ARS databases and genomics projects at Ithaca and Cold Spring Harbor, NY; Beltsville, MD; and Ames, IA. It will include field-based phenotyping at Lubbock, TX, and translation into biology- enabled crop breeding. It will include the assessment of community needs, development of workshops and training material to support stakeholder engagement, and development of standards. Thus, sorghum is a model for addressing extremely urgent stakeholder needs in the field through the application of traditional marker assisted strategies and the application of new biology-enabled models for crop breeding. This is the final report for project 3096-21000-020-00D, which terminated in March 2018 and replaced with new project 3096-21000-021-00D. All planned field experiments were completed prior to the start of FY2018; no new experiments were initiated in the time frame corresponding to this project. During the last five years, progress was made in all subobjectives and all milestones were fully-met or substantially met. Significantly, new screening tools were developed to screen natural sorghum germplasm collections and induced mutant populations for abiotic stress tolerance. New sorghum accessions with improved cold tolerance and drought tolerance were discovered and released publicly through publications in Journal of Plant Registrations. New sugarcane aphid-resistant breeding lines with drought tolerance and good grain yield potential were released, which provide much-needed inbred lines to improve sugarcane aphid resistance. A new method to identify causal genes for important agronomic traits was developed and was applied to identify three genes that confer the multi- seeded (msd) phenotype in sorghum. The msd mutants have the potential to triple the seed number and double the seed weight per panicle in increasing the fertility of all sorghum flowers. Furthermore, the molecular mechanism of Msd1 gene was found to regulate the abortion of sorghum flowers by triggering programmed cell death pathway through induction of jasmonic acid during panicle development. The mutations in the Msd1 gene prevent the programmed cell death pathway and lead to seed setting in all flowers. This achievement discovered new approaches to increase grain yield in sorghum, as well as, in other cereals. Moreover, the ARS scientists at Lubbock, Texas all also completed whole genome sequencing of 256 selected mutant lines. The sequenced lines possess >1.8 million ethylmethane sulfonate-induced (EMS) mutations that cover 95% of the genes in the sorghum genome, providing the sorghum communities worldwide a reverse genetic resource to study the function of sorghum genes. Accomplishments 01 Identification of a mechanism for the abortion of the pedicellate spikelets in sorghum. Like many other cereal crops, sorghum panicle produces two types of spikelet. The one type of spikelets invariably abort in natural sorghum lines, as well as in many other cereal crops. However, the mechanism for the abortion is not known. ARS scientists at Lubbock, Texas, identified and characterized the gene Msd1, a master regulator of the development of the pedicellate spikelets that tend to abort. This discovery may lead to new approaches to increase the grain yield of sorghum, as well as other cereal crops, by increasing seed numbers. 02 Release of two sugarcane aphid resistant sorghum lines. Sugarcane aphids (SCA) have become a major pest and threaten sorghum production in the entire U.S. New breeding lines that are SCA tolerant are urgently needed. ARS scientists at Lubbock, Texas, bred and publicly released two sorghum breeding lines, R.LBK1 and R.LBK2, which exhibit high grain yields and other favorable agronomic traits. The two lines have been transferred to five seed companies and are currently being evaluated for breeding hybrids in the Texas and Kansas grain sorghum performance trials. 03 Development of pollinator line with multi-seeded (msd) trait. Grain number is a major determinant of grain yield. Previously, a series of multi-seeded msd mutants that have the potential to triple the seed number per panicle from the inbred line BTx623 have been developed. To make sorghum hybrids with the msd trait, the mutation from BTx623, a female parent, must be also introduced to a male parent (pollinator) in hybrid breeding. ARS scientists in Lubbock, Texas have developed a pollinator, RTx437, with the msd trait that is 94% identical to the original RTx437 genome. This will enable sorghum breeder to test if the msd trait will increase grain yield in sorghum hybrids 04 Identification of three genes involved in the production of epidermal wax. The sorghum plant produces an abundant amount of delicate epidermal wax but these compounds are easily dislodged from the stem or leaves. To optimize the protective capacity of epidermal wax, there is a need to modify the wax structure so it will adhere to the epidermis. ARS scientists at Lubbock, Texas, analyzed the genetics and physiology of sorghum mutants with reduced or absent epidermal wax and subsequently identified a set of three genes that are necessary for epidermal wax synthesis. Sorghum lines harboring variants of these genes can be deployed as new germplasm sources for the improvement of resilience against moisture stress, pathogen or insect attack in sorghum. 05 Identification of high and low dhurrin sorghum hybrids. Dhurrin is a cyanogenic glucoside that can cause cyanide poisoning in livestock under specific conditions, but also a metabolite associated with post- flower drought tolerance in sorghum. However, the dhurrin content in the U.S. hybrids is not known. ARS scientists in Lubbock, Texas, evaluated a set of grain sorghum hybrids and identified significant variation for dhurrin content. Dhurrin levels in hybrids are related to that of the inbred parents. Although dhurrin levels variated significantly among sorghum hybrids, levels were below the threshold considered dangerous at the time of plant maturity, indicating that grain sorghum hybrids with moderate levels of leaf dhurrin can be safely utilized for cattle grazing late in the season. These findings provide critical information for breeding drought tolerant sorghum hybrids with the concern for safe grazing. 06 Development and characterization of a cold tolerant population for sorghum improvement. Cold or chilling tolerance is recognized as a key trait for sorghum improvement to accomplish early season planting and boost water use efficiency during the season. ARS scientists at Lubbock, Texas, developed an advanced generation of 292 recombinant inbred lines with parentage of BTx623 and Niu Sheng Zui and released these inbred lines for public dissemination through the ARS Genetic Resource Information Network. Inbred lines with outstanding cold tolerance have the potential to serve as seed parents for the transfer of chilling tolerance to elite sorghum breeding lines.
Impacts
(N/A)
Publications
- Xin, Z., Chen, J., Jiao, Y., Gladman, N., Hayes, C.M., Burow, G.B., Emendack, Y., Burke, J.J. 2018. Registration of BTx623ms8 - a new and easily identifiable nuclear male sterile mutant in sorghum. Journal of Plant Registrations. doi:10.3198/jpr2017.09.0063crgs.
- Jiao, Y., Burow, G.B., Gladman, N., Acosta Martinez, V., Chen, J., Burke, J.J., Ware, D., Xin, Z. 2018. Efficient identification of causal mutations through sequencing of bulked F2 from two allelic bloomless mutants. Frontiers in Plant Science. doi.org/10.3389/fpls.2017.02267.
- Burke, J.J., Emendack, Y., Hayes, C.M., Chen, J. 2018. Genetic diversity in the environmental conditioning of two sorghum (Sorghum bicolor L.) hybrids. American Journal of Plant Sciences. 9:817-831.
- Burke, J.J. 2017. Genetic diversity in the environmental conditioning of gossypium hirsutum and gossypium barbadense cultivars. American Journal of Plant Sciences. 8(3):517-532.
- Gitz, D.C., Liu Gitz, L., Xin, Z., Baker, J.T., Payton, P.R., Lascano, R.J. 2017. Description of a novel allelic �thick leafed� mutant of sorghum. American Journal of Plant Sciences. 8:2956-2965.
- Marla, S.R., Welti, R., Shiva, S., Liu, S., Burke, J.J., Morris, G. 2017. Comparative transcriptome and lipidome analyses reveal molecular systems underlying chilling response in chilling-tolerant sorghums. The Plant Genome. 10:1-16. doi:10.3835/plantgenome2017.03.0025.
- Limaje, A., Hayes, C., Armstrong, J.S., Hoback, W., Zarrabi, A., Paudyal, S., Burke, J. 2018. Antibiosis and tolerance discovered in USDA-ARS sorghums resistant to the sugarcane aphid (Hemiptera: Aphididae). Journal of Entomological Science. 53(2):230-241.
- Wang, C., Ulloa, M., Duong, T., Robert, P. 2018. Quantitative trait loci mapping of multiple independent loci for resistance to fusarium oxysporum f. sp. vasinfectum races 1 and 4 in an interspecific cotton population. Journal of Phytopathology. 108:759-767.
- Witt, T.W., Ulloa, M., Pelletier, M.G., Mendu, V., Ritchie, G.L. 2018. Exploring ethyl methaneSulfonate (EMS) treated cotton (Gossypium hirsutum L.) to improve drought tolerance. Euphytica. 214:123.
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Progress 10/01/16 to 09/30/17
Outputs
Progress Report Objectives (from AD-416): The long-term objective of this plan is to develop sorghum inbred lines that possess superior tolerance to abiotic stresses, and high biomass and grain yield potential. We will integrate natural variation, induced mutation, phenotype-based and marker-assisted selection to identify the desirable traits and introduce them into elite sorghum inbred lines. Specifically, during the next 5 years we will focus on the following objectives: Objective 1: Develop new screening tools and genetic resources to identify sorghum lines with high grain or biomass yield potential under drought and temperature stresses. Subobjective 1A: Evaluate the relationship between dhurrin concentrations and the staygreen trait. Subobjective 1B: Evaluate the diversity of the stay-green trait among sorghum germplasm collections. Subobjective 1C: Evaluate the efficacy of stay-green markers in F1 hybrids. Objective 2: Identify novel sources of genetic variation for cold temperature and drought tolerance in sorghum. Subobjective 2A: Develop high resolution genetic and QTL maps using new ARS mapping populations to discover robust and effective DNA markers conditioning early season cold tolerance, and validate marker-assisted selection using a subset of cold tolerant inbreds. Subobjective 2B: Identify markers or genes associated with high seed number and erect leaf traits. Objective 3: Develop improved grain sorghum and non-grain, energy sorghum breeding lines with high grain or biomass yield potential under high abiotic stress environments. Subobjective 3A: Develop and release novel ARS germplasm with enhanced abiotic stress traits such as stay-green, cold tolerance, high grain number, and erect leaf traits. Objective 4: Accelerate sorghum community trait analysis and trait development, via a new USDA public sorghum crop genome database system, by providing open access to sorghum genome sequence information, germplasm diversity information, trait mapping information, and phenotype information, with an initial emphasis on sugarcane aphid resistance. [NP301, C4, PS4A, C1, PS1A, C2, PS2A, C3, PS3A] Approach (from AD-416): Superior traits that enhance sorghum grain and biomass yield and abiotic stress tolerance, identified previously from mutation population and natural germplasm collections, will be mapped using classical genetic analysis and the state-of- art Next-Generation Sequencing technology. Molecular markers will be developed for the rapid introgression of these traits into elite commercial lines. Lines with high yield potential and superior resilience to abiotic stresses will be developed through a systematic approach integrating physiology, marker-assisted selection, and conventional breeding. This project will provide much needed support for sorghum genomic and genetic research and germplasm improvement. Sorghum is an important feed, biofuel, and food crop in the United States. It is a superior heat and drought resistant crop, and thus its importance for U.S. agriculture is increasing given the impacts of global warming and water scarcity. However, production losses caused by increasing pressure from the sugarcane aphid pest have recently slowed the growth of sorghum production. Thus, increased support for sorghum genomic, genetic, and germplasm information generation and sharing is urgently needed to accelerate the rate of improvement in high-value target traits. To meet this critical need, a new USDA-ARS public sorghum genomics and genetics database will be developed to increase information management capacity, promote open access data and information sharing, and open access to data analysis tools; to facilitate the development and implementation of standardized methods for the collection, analysis, and utilization of new sorghum data; and to enable sorghum researchers and breeders to accelerate the development of superior performing cultivars for U.S. producers. The project will leverage strategic biology-enabled information at USDA-ARS databases and genomics projects at Ithaca and Cold Spring Harbor, NY; Beltsville, MD; and Ames, IA. It will include field-based phenotyping at Lubbock, TX, and translation into biology- enabled crop breeding. It will include the assessment of community needs, development of workshops and training material to support stakeholder engagement, and development of standards. Thus, sorghum is a model for addressing extremely urgent stakeholder needs in the field through the application of traditional marker assisted strategies and the application of new biology-enabled models for crop breeding. Under Objective 1, we made significant progress in developing new screening tools for cold and drought tolerance. Under Objective 2, we made progress in identifying new sources for cold and drought tolerance. Under Objective 3, we released several new lines with drought tolerance and sugarcane aphid resistance. These lines have been adopted by several companies in their breeding program through a Material Transfer Agreement. Under Objective 4, we have published the sequencing of 256 selected mutant lines. The mutation data can be searched on Gramene (http://www. gramene.org ). Several thousand lines have been shared with private industries and public institutes through a Material Transfer Agreement. Accomplishments 01 Developed two sugarcane resistant sorghum pollinators (R lines). Sugarcane aphid has become a major pest in sorghum in the last few years. ARS scientists at Lubbock, Texas, developed two new pollinator (restorer or R) lines designated LBK1 and LBK2 (tested as R.11259 and R. 11143) that showed significant tolerance to sugarcane aphid. These R lines can help breeding sorghum hybrids resistant to sugarcane aphid. These two lines have been transferred to four seed companies via Material Transfer Agreements (MTAs) and have been adopted in their breeding program. 02 Development of new sorghum lines with enhanced grain number. Grain number per panicle is a major determinant of grain yield. ARS scientists at Lubbock, Texas, have developed new sorghum lines with increased seed number through marker-assisted breeding. To date, BC4 introgression of the multi-seeded trait was accomplished in both A/ BTx399 and RTx430 by marker-assisted breeding. These new lines are now being evaluated for development of hybrid combinations aimed to increase grain yield of sorghum. 03 Molecular markers for thermal stress identified through translational genomics. High temperature is a major stress depressing sorghum yield, but evaluation of high temperature tolerance is complicated and requires the high temperature stress occurring at the exact development stages. Scientists from USDA-ARS Lubbock, Texas, analyzed the genetic variation associated with responses to thermal stresses in a sorghum association panel (SAP) representing major races and working groups to identify single nucleotide polymorphisms (SNPs) that are associated with resilience to temperature stress in a major cereal crop. Genome- wide analyses identified thirty SNPs that were strongly associated with traits measured at seedling stage under cold stress and tagged genes that act as regulators of anthocyanin expression and soluble carbohydrate metabolism. Validation of the predictive value of the significant SNP markers was initiated. These findings could provide foundation for use of haplotypes for development of temperature resilient sorghum cultivars and further characterization of genes and their networks responsible for adaptation to thermal stresses. 04 Identified a new easily recognizable sorghum nuclear male sterile mutant. Nuclear male sterile lines are important tools for population improvement and evaluation of potential of breeding lines. ARS scientists at Lubbock, Texas, have identified a new nuclear male sterile mutant (ms8) that can be easily recognized at early stage of the anthesis. The male sterile phenotype is stable under multiple environments. The ms8 mutant can be used as an important tool to backcross sorghum mutants and as a parent for population improvement through random mating. The mutant has been transferred to several ARS scientists and academic scientists through MTA. 05 Release of 4 sorghum lines with cold tolerance and drought tolerance. Cold tolerance has been voted as an important trait for sorghum improvement for early planting to take the advantage early season moisture. ARS scientists at Lubbock, Texas, have developed four-grain sorghum germplasm lines, PSLS-SGCTB01, PSLS-SGCTR02, PSLS-SGCTB03, and PSLS-SGCTB04 that possess excellent post-flowering drought tolerance based upon the stay-green trait and excellent early-season cold tolerance. These lines have large potential in developing sorghum hybrids that are drought tolerant and can be planted early under cold temperatures.
Impacts
(N/A)
Publications
- Chopra, R., Burow, G.B., Chagoya, J., Simpson, C., Mudge, J., Burow, M. 2016. Transcriptome sequencing of diverse peanut (arachis) wild species and the cultivated species reveals a wealth of untapped genetic variability. Genes, Genomes, Genetics. 6:3825-3827.
- Emendack, Y., Chopra, R., Hayes, C.M., Sanchez, J., Burow, G.B., Xin, Z., Burke, J.J. 2016. Early seedling growth characteristics relates to the stay-green traits and dhurrin levels in sorghum. Crop Science. 57:1-12.
- Xin, Z., Huang, J., Smith, A., Chen, J., Burke, J.J., Sattler, S.E., Zhao, D. 2017. Morphological characterization of a new and easily recognizable nuclear male sterile mutant of sorghum (Sorghum bicolor). PLoS One. 12(1) :1-14.
- Chopra, R., Burow, G.B., Burke, J.J., Xin, Z., Gladman, N. 2017. Genome wide association analysis for seedling response traits to thermal stress in sorghum germplasm. Biomed Central (BMC) Plant Biology. 17:12. doi:10. 1186/s12870-016-0966-2.
- Zhang, K., Zheng, G., Saul, K., Xin, Z., Jiao, Y., Wang, D. 2017. Evaluation of the multi-seeded (msd) mutant of sorghum for ethanol production. Industrial Crops and Products. 97:345-353.
- Shen, Y., Ruan, O., Chai, H., Yuan, Y., Yang, W., Chen, J., Xin, Z., Shi, H. 2016. The arabidopsis polyamine transporter LHRI/AtPUT3 modulates heat responsive gene expression by regulating mRNA stability. Plant Journal. 88(6):1006-1021.
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Progress 10/01/15 to 09/30/16
Outputs
Progress Report Objectives (from AD-416): The long-term objective of this plan is to develop sorghum inbred lines that possess superior tolerance to abiotic stresses, and high biomass and grain yield potential. We will integrate natural variation, induced mutation, phenotype-based and marker-assisted selection to identify the desirable traits and introduce them into elite sorghum inbred lines. Specifically, during the next 5 years we will focus on the following objectives: Objective 1: Develop new screening tools and genetic resources to identify sorghum lines with high grain or biomass yield potential under drought and temperature stresses. Subobjective 1A: Evaluate the relationship between dhurrin concentrations and the staygreen trait. Subobjective 1B: Evaluate the diversity of the stay-green trait among sorghum germplasm collections. Subobjective 1C: Evaluate the efficacy of stay-green markers in F1 hybrids. Objective 2: Identify novel sources of genetic variation for cold temperature and drought tolerance in sorghum. Subobjective 2A: Develop high resolution genetic and QTL maps using new ARS mapping populations to discover robust and effective DNA markers conditioning early season cold tolerance, and validate marker-assisted selection using a subset of cold tolerant inbreds. Subobjective 2B: Identify markers or genes associated with high seed number and erect leaf traits. Objective 3: Develop improved grain sorghum and non-grain, energy sorghum breeding lines with high grain or biomass yield potential under high abiotic stress environments. Subobjective 3A: Develop and release novel ARS germplasm with enhanced abiotic stress traits such as stay-green, cold tolerance, high grain number, and erect leaf traits. Approach (from AD-416): Superior traits that enhance sorghum grain and biomass yield and abiotic stress tolerance, identified previously from mutation population and natural germplasm collections, will be mapped using classical genetic analysis and the state-of- art Next-Generation Sequencing technology. Molecular markers will be developed for the rapid introgression of these traits into elite commercial lines. Lines with high yield potential and superior resilience to abiotic stresses will be developed through a systematic approach integrating physiology, marker-assisted selection, and conventional breeding. In 2016, progress was made on many fronts. The most significant achievement is the completion of the analysis the whole genome sequencing data for 256 selected sorghum mutant lines, providing the sorghum community an unprecedented genomic resource (Objective 1). Another new gene for the multiseeded (msd) mutants was identified (Objective 2B). New QTLs for drought tolerance (dhurrin accumulation), cold tolerance, and high temperatures tolerance were identified (Objective 1A). Molecular markers were developed for accelerated incorporation of these traits into elite lines (Objective 1B). Two recombinant inbred (RI) populations for mapping cold tolerance were released (Objective 2A). Accomplishments 01 Completed analysis for whole genome sequencing of 256 mutant sorghum lines. In collaboration with ARS lab in Cold Spring Harbor, researchers in the Plant Stress and Germplasm Development Research Unit in Lubbock, Texas, completed the data analysis of whole genome sequencing for 256 randomly selected mutant sorghum lines. The mutation data produced 1.8 million high quality ethyl methane sulfonate-induced mutations affecting 95% of the genes in sorghum genome. This data provide a genomic resource for sorghum and other C4 grain and bioengergy crops. The result is published in Plant Cell (available online). 02 Identified the MSD3 gene that has the potential to increase grain number and enhance grain yield in sorghum. Researchers in the Plant Stress and Germplasm Development Research Unit in Lubbock, Texas, isolated a collection of sorghum mutants that have the potential to triple the seed number and double the seed weight per panicle. After identification of two of the msd1 and msd2 genes previously, they identified another gene, msd3, in 2016. These genes provided new tools to improve sorghum grain yield. 03 Formal release and deposit of �Cool� sorghums-- diverse mapping populations' improvements with cold tolerance traits and its public availability thru the Germplasm Resources Information Network (www.ars- grin.gov/npgs). The United States is the leading sorghum producer in the world, but early season planting and stand establishment is hampered by cool soil and ambient temperature in the U.S. sorghum belt during early late March to early April. Planting at early season is more than ever needed by farmers to adapt to climatic changes, avail of spring moisture and aid in realizing higher yield using longer growing season cultivars. ARS researchers at Lubbock, Texas, developed, released, and characterized two recombinant inbred populations that exhibit an overall increased germinability at cooler soil and ambient temperatures between the temperatures of 55-58F (14-16C). The populations offer wide diversity for improvement of cold tolerance, seed quality, and desirable agronomic qualities. The population was distributed to university breeding programs for evaluation and use as parental resource for breeding for early season cold tolerance. 04 Development and validation of allele-specific markers for thermal stress response in sorghum through combined approach of genome-wide association mapping and validation of gene-based variation. Translational genomics is a new field that aims to pinpoint and utilize nucleotide variation between sorghum germplasm thru validation of variation and convert this information into easy access DNA markers for application in molecular and marker assisted breeding. ARS researchers in Lubbock, Texas, integrated transcriptome profiling with the development of a catalog of validated nucleotide variation to differences in responsive genes among sorghum germplasm under cold stress. The results provide an insight into the mechanisms involved in cold response of sorghum that can be applied for development of cold tolerant cultivars of cereal crops. The DNA variation identified between the tolerant and sensitive lines are needed and will greatly aid in precise selection of recombinant inbred lines or germplasm for breeding early-season cold tolerant cultivars. 05 Translational genomics leads to identification of robust and stable single nucleotide polymorphic (SNP) markers for use in selection and breeding of brown midrib trait in forage and bioenergy sorghums. There is a need to transform nucleotide variation data between sorghum germplasm into easy access genetic markers for molecular and marker- assisted breeding that can be used by seed companies and public researchers. ARS scientists from Lubbock, Texas, and Lincoln, Nebraska, joined together to utilize genomic data for genes in monolignol pathway to identify robust and stable SNP markers for the brown midrib phenotype, an important trait, which is associated with reduced lignin content and greater ethanol conversion efficiency. Development and testing of functional assays resulted in efficient and highly penetrant and stable variant DNA marker for bmr6 and bmr12 that provide a platform to screen for the variation in brown midrib trait present in diverse lines and contribute to an opportunity to identify new alleles for improvement of biomass crops. 06 Genetic analysis of profuse bloom wax leads to identification of genes and alleles specific markers for wax production in sorghum. An important feature of sorghum that is associated with drought tolerance is that of wax compounds that covers and protects the stem and underside of leaves. However, there is lack of genetic information on genes that underlie important wax production in sorghum. ARS researchers from Lubbock, Texas, in cooperation with Cold Spring Harbor scientists identified two genes that underpin profuse wax or bloom of sorghum. This discovery is highlighted in the high impact manuscript published in �The Plant Cell�. Discovery of genes for bloom/wax will allow the manipulation of the trait to improve drought and heat tolerance in sorghum with implications to other cereal crops. 07 Deployment of genetic markers for marker assisted rapid trait introgression (MARTI) of novel multi-seeded trait to enhance grain yield in sorghum. Seed number is a major determinant of grain yield in sorghum and other cereal crops. ARS researchers in Lubbock, Texas, in collaboration with researchers from Cold Spring Harbor Laboratory, NY, developed novel and precise genetic markers that are easy to use for swift and precise detection of the multi-seeded trait at seedling stage and recently were demonstrated as a useful tool for molecular breeding of the trait to elite lines. The markers are being deployed thru the MARTI pipeline and swift development of near isogeneic line versions of elite sorghum with the msd trait will be delivered. 08 Discovery of a dhurrin quantitative trait loci (QTL) as a novel stay- green QTL. Dhurrin is a cyanogenic glucoside produced by sorghum and is generally considered a natural defense compound capable of producing the toxin hydrogen cyanide (HCN) to deter animal herbivory. Recently, ARS scientists from Lubbock, Texas, reported that high levels of leaf dhurrin in grain sorghum genotypes was correlated with post-flowering drought tolerance (stay-green). Post-flowering drought tolerance is associated with reduced lodging, charcoal rot resistance, increased grain fill, and increased grain yield. ARS scientists from Lubbock, Texas, recently discovered a dhurrin QTL (Dhu1) on SBI01 using a recombinant inbred line (RIL) mapping population derived from BTx642/ Tx7000. Leaf dhurrin was highly heritable and Dhu1 explained a large percentage of the variation of leaf dhurrin in the population. Dhu1 is aligned with genes involved in dhurrin biosynthesis (CYP79A1, CYP71E1, UGT85B1). Protein sequence variants found in CYP71E1 and UGT85B1 appear to be the cause of the observed differences in leaf dhurrin levels in many sorghum lines that vary in leaf dhurrin content. Dhu1 is also aligned with a novel stay-green QTL (Stg5) on SBI01, consistent with prior studies showing an association between high leaf dhurrin levels, this region of SBI01, and expression of the stay-green trait. 09 Population studies identified genes for range of thermal stress. Climate variability due to fluctuation in temperature is a worldwide concern that imperils crop production. Scientists from USDA-ARS Lubbock, Texas, analyzed the genetic variation associated with responses to thermal stresses in a sorghum association panel (SAP) representing major races and working groups to identify single nucleotide polymorphisms (SNPs) that are associated with resilience to temperature stress in a major cereal crop. Genome-wide analyses identified thirty SNPs that were strongly associated with traits measured at seedling stage under cold stress and tagged genes that act as regulators of anthocyanin expression and soluble carbohydrate metabolism. Meanwhile, 12 SNPs were found significantly associated with seedling traits under heat stress and these SNPs tagged genes that function also in sugar metabolism, and ion transport pathways. These findings could provide foundation for use of haplotypes for development of temperature resilient sorghum cultivars and further characterization of genes and their networks responsible for adaptation to thermal stresses.
Impacts
(N/A)
Publications
- Chopra, R., Burow, G.B., Hayes, C.M., Emandack, Y., Burke, J.J., Xin, Z. 2015. Transcriptome profiling and validation of gene based single nucleotide polymorphism (SNP) markers in sorghum genotypes with contrasting response to cold stress. Biomed Central (BMC) Genomics. 16:1- 11.
- Roy, S., Cho, S., Kwon, S., Kamal, A.M., Kim, S., Oh, M., Lee, M., Chung, K., Xin, Z., Woo, S. 2016. Morpho-physiological and proteome level responses to cadmium stress in sorghum. PLoS One. 11(2):e0150431. doi:10. 1371/journal.pone.0150431.
- Burow, G.B., Franks, C., Burke, J.J., Xin, Z., Pederson, G.A. 2016. Registration of RTx430/gaigaoliang sorghum [sorghum bicolor (L.) moench recombinant inbred line mapping population. Journal of Plant Registrations. 10:206-209.
- Roy, S., Cho, S., Kwon, S., Kamal, A., Kim, S., Oh, M., Sarker, K., Lee, M. , Chung, K., Xin, Z., Woo, S. 2016. Leaf proteome characterization in the context of physiological and morphological changes in response to copper stress in sorghum. BioMetals. 29(3):495-513.
- Scully, E.D., Gries, T.L., Funnell-Harris, D.L., Xin, Z., Kovacs, F.A., Vermerris, W., Sattler, S.E. 2016. Characterization of novel Brown midrib 6 mutations affecting lignin biosynthesis in sorghum. Journal of Integrative Plant Biology. 58:136-149. doi:10.1111/jipb.12375.
- Adeyanju, A., Yu, J., Little, C., Rooney, W., Klein, P., Burke, J.J., Tesso, T. 2016. Sorghum recombinant inbred lines segregating for stay- green QTL's and leaf dhurrin content show differential reaction to stalk rot diseases. Crop Science. doi:10.2135/cropsci2015.10.0628..
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Progress 10/01/14 to 09/30/15
Outputs
Progress Report Objectives (from AD-416): The long-term objective of this plan is to develop sorghum inbred lines that possess superior tolerance to abiotic stresses, and high biomass and grain yield potential. We will integrate natural variation, induced mutation, phenotype-based and marker-assisted selection to identify the desirable traits and introduce them into elite sorghum inbred lines. Specifically, during the next 5 years we will focus on the following objectives: Objective 1: Develop new screening tools and genetic resources to identify sorghum lines with high grain or biomass yield potential under drought and temperature stresses. Subobjective 1A: Evaluate the relationship between dhurrin concentrations and the staygreen trait. Subobjective 1B: Evaluate the diversity of the stay-green trait among sorghum germplasm collections. Subobjective 1C: Evaluate the efficacy of stay-green markers in F1 hybrids. Objective 2: Identify novel sources of genetic variation for cold temperature and drought tolerance in sorghum. Subobjective 2A: Develop high resolution genetic and QTL maps using new ARS mapping populations to discover robust and effective DNA markers conditioning early season cold tolerance, and validate marker-assisted selection using a subset of cold tolerant inbreds. Subobjective 2B: Identify markers or genes associated with high seed number and erect leaf traits. Objective 3: Develop improved grain sorghum and non-grain, energy sorghum breeding lines with high grain or biomass yield potential under high abiotic stress environments. Subobjective 3A: Develop and release novel ARS germplasm with enhanced abiotic stress traits such as stay-green, cold tolerance, high grain number, and erect leaf traits. Approach (from AD-416): Superior traits that enhance sorghum grain and biomass yield and abiotic stress tolerance, identified previously from mutation population and natural germplasm collections, will be mapped using classical genetic analysis and the state-of- art Next-Generation Sequencing technology. Molecular markers will be developed for the rapid introgression of these traits into elite commercial lines. Lines with high yield potential and superior resilience to abiotic stresses will be developed through a systematic approach integrating physiology, marker-assisted selection, and conventional breeding. The relationship between dhurrin concentrations and the stay-green trait were evaluated in 400 sorghum lines from the sorghum conversion program. Selected lines exhibiting high and with low dhurrin were evaluated for differential responses to post-flowering water-deficit stress. Clear differences in leaf and plant death ratings were observed. Lines having low dhurrin levels had greater leaf senescence compared with the high dhurrin lines. Sorghum lines from the Sudan collection that were identified as potential stay-green lines from a stress bioassay using chlorophyll fluorescence were confirmed based upon leaf dhurrin levels. Two lines were further advanced in our breeding program and are currently being evaluated for a germplasm release. Identified and cloned genes from sorghum that more than double the seed number per panicle. Concomitant with gene cloning, novel and precise genetic marker that are easy to use for swift and precise detection of the multi-seeded trait at seedling stage were developed and recently was demonstrated as useful tool for molecular breeding of the trait to elite sorghums. Developed and registered a new genetic mapping population, RTx430 x PI610727 recombinant inbred population that exhibit an overall increased germinability at cold soil and ambient temperatures between the range of 55-58�F (14-16�C). Utilized DNA sequence data for lignin biosynthesis to identify precise genetic markers for the brown midrib phenotype, an important trait, which is associated with reduced lignin content and greater ethanol conversion efficiency. A comprehensive set of precise and easy to use molecular markers for brown midrib trait mined from both induced and spontaneous (natural) variation were developed, validated and tested to provide a platform to screen for the variation in brown midrib trait present in diverse lines and contribute an opportunity to identify new alleles for improvement of biomass crops. Accomplishments 01 Two genes increasing seed number in sorghum identified. ARS researchers at Lubbock, TX identified two genes that can double the seed number and significantly enhance the seed weight per panicle (head) in sorghum. Seed number per panicle is a major determinant of grain yield in sorghum and other cereal crops. From the sorghum mutant library established at the Plant Stress and Germplasm Research Unit, several multiseeded (msd) mutants that have potential to increase grain yield were isolated previously, and in collaboration with ARS researchers at Cold Spring Harbor, NY, two genes underlying the msd trait were identified through next-generation sequencing. Two patents detailing the inventions were filed. The msd mutants have been distributed to eight breeding companies to develop high yield sorghum hybrids. 02 Perfect molecular markers to select multiseeded traits developed. ARS researchers in Lubbock, TX developed precise molecular markers based on the cloned genes that can double the seed number per panicle. Marker- assisted selection can accelerate the breeding process. Most markers based on other genetic approaches are usually too far away to be effective selection markers, but molecular markers developed according to the cloned genes are right on the gene and can select the trait at early seedling stage with 100% accuracy. The genes and markers discovered are now being utilized by the seed industry to rapidly incorporate the multiseeded trait into their proprietary lines. 03 Mapping population for cold tolerance registered. The United States is the leading sorghum producer in the world, but stand establishment is hampered by cold soil and ambient temperature in the US sorghum belt during early season. Planting at early season is needed to fully use the early season soil moisture reserve and to realize higher yield with longer growing season cultivars. ARS researchers at Lubbock, TX developed and registered a new genetic mapping population, RTx430 x PI610727 recombinant inbred population that exhibits an overall increased germinability at cold soil and ambient temperatures between the range of 55-58�F (14-16�C). Selected lines from this population were distributed to three sorghum seed companies and two universities for evaluation and use as parent for breeding early season cold tolerance. 04 Dhurrin content was evaluated in 700 diverse sorghum lines as a trait for drought tolerance. Dhurrin is usually considered as an undesirable metabolite because it can produce prussic acid (HCN) that is toxic to cattle. However, it was discovered as an important attribute that contributes toward post-flowering drought tolerance in a number of sorghum lines. ARS researchers from Lubbock, TX in collaboration with University cooperators at University of Illinois evaluated the dhurrin content in 700 unique sorghum lines and associated dhurrin levels with genome-wide DNA sequence variation in these lines with a technique known as �genome wide association analysis�. The study discovered a total of 19 genetic markers associated with dhurrin accumulation, involving both dhurrin biosynthesis and metabolism genes. The results firmly established dhurrin as an attribute to post-flowering drought tolerance and provide molecular markers for selection of either high or low dhurrin accessions based on breeding objectives. 05 Novel grain sorghum lines with enhanced cold tolerance identified. Sorghum is a grass species of tropical origin that is utilized throughout the world as a food, feed, and biofuel crop. Being of tropical origin, sorghum is sensitive to cold conditions, especially temperatures below 60� F. Cold tolerance in sorghum has been observed before in some breeding lines of Chinese descent, but these lines are too tall and exotic to be fully utilized in a grain breeding program in the United States. ARS researchers in Lubbock, TX evaluated over 2000 sorghum conversion (SC) and exotic (PI) lines and identified a subset of materials (100-150) that germinate and grow under cold conditions below 60� F. The new sources of cold tolerance are shorter in height, have better grain yield potential, and are desired by the seed industry.
Impacts
(N/A)
Publications
- Chopra, R., Burow, G.B., Simpson, C., Farmer, A., Mudge, J., Burow, M. 2014. Comparisons of de novo transcriptome assemblers in diploid and polyploid species using peanut (Arachis spp.) RNA-seq data. PLoS One. DOI: 10.1371/journal.pone.0115055.
- Emendack, Y., Malinowski, D., Burke, J.J., Burow, G.B., Xin, Z. 2014. Morpho-physiological characterization of cold-and pre-flowering drought tolerance in grain Sorghum (Sorghum bicolor L. Moench) inbreds. American Journal of Experimental Agriculture. 4(12):1500-1516.
- Burke, J.J., Payton, P.R., Chen, J., Xin, Z., Burow, G.B., Hayes, C.M. 2015. Metabolic responses of two contrasting sorghums to water-deficit stress. Crop Science. 55:344-353.
- Chopra, R., Burow, G.B., Chamberlin, K.D., Burow, M. 2015. Next-generation transcriptome sequencing, SNP discovery, and SNP validation in four market classes of peanut, arachis hypogaea L. Molecular Genetics and Genomics. 290(3):1169-1180.
- Hayes, C.M., Burow, G.B., Brown, P., Burke, J.J., Xin, Z., Thurber, C. 2015. Natural variation in synthesis and catabolism genes influences dhurrin content in sorghum (Sorghum bicolor L. Moench). The Plant Genome. 8(2):1-9.
- Xin, Z., Gitz, D.C., Burow, G.B., Hayes, C.M., Burke, J.J. 2015. Registration of two allelic erect leaf mutants of sorghum. Journal of Plant Registrations. 9:254-257.
- Gitz, D.C., Baker, J.T., Burke, J.J., Xin, Z., Lascano, R.J. 2015. The microenvironment within and pollen transmission through paper and polyethylene sorghum pollination bags. American Journal of Plant Sciences. 6:265-274.
- Wang, M.L., Cole, M.R., Tonnis, B.D., Pinnow, D.L., Xin, Z., Davis, J., Hung, Y., Yu, J., Pederson, G.A., Eggleston, G. 2014. Comparison of stem damage and carbohydrate composition in the stem juice between sugarcane and sweet sorghum harvested before and after late fall frost. Journal of Sustainable Bioenergy Systems (JSBS). 4:161-174.
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Progress 10/01/13 to 09/30/14
Outputs
Progress Report Objectives (from AD-416): The long-term objective of this plan is to develop sorghum inbred lines that possess superior tolerance to abiotic stresses, and high biomass and grain yield potential. We will integrate natural variation, induced mutation, phenotype-based and marker-assisted selection to identify the desirable traits and introduce them into elite sorghum inbred lines. Specifically, during the next 5 years we will focus on the following objectives: Objective 1: Develop new screening tools and genetic resources to identify sorghum lines with high grain or biomass yield potential under drought and temperature stresses. Subobjective 1A: Evaluate the relationship between dhurrin concentrations and the staygreen trait. Subobjective 1B: Evaluate the diversity of the stay-green trait among sorghum germplasm collections. Subobjective 1C: Evaluate the efficacy of stay-green markers in F1 hybrids. Objective 2: Identify novel sources of genetic variation for cold temperature and drought tolerance in sorghum. Subobjective 2A: Develop high resolution genetic and QTL maps using new ARS mapping populations to discover robust and effective DNA markers conditioning early season cold tolerance, and validate marker-assisted selection using a subset of cold tolerant inbreds. Subobjective 2B: Identify markers or genes associated with high seed number and erect leaf traits. Objective 3: Develop improved grain sorghum and non-grain, energy sorghum breeding lines with high grain or biomass yield potential under high abiotic stress environments. Subobjective 3A: Develop and release novel ARS germplasm with enhanced abiotic stress traits such as stay-green, cold tolerance, high grain number, and erect leaf traits. Approach (from AD-416): Superior traits that enhance sorghum grain and biomass yield and abiotic stress tolerance, identified previously from mutation population and natural germplasm collections, will be mapped using classical genetic analysis and the state-of- art Next-Generation Sequencing technology. Molecular markers will be developed for the rapid introgression of these traits into elite commercial lines. Lines with high yield potential and superior resilience to abiotic stresses will be developed through a systematic approach integrating physiology, marker-assisted selection, and conventional breeding. In FY2014, scientists in Lubbock, Texas, successfully identified two genes associated with high yield potential sorghum multiseeded (msd) mutants, completed screening of 376 Sudanese sorghum germplasm collection for post-flowering drought tolerance, phenotyped three new mapping populations for early season cold tolerance, and made over 400 hundred crosses of msd, cold, and drought tolerance traits into elite B and R breeding lines. Accomplishments 01 New drought-tolerant lines identified from Sudanese sorghum germplasm collection. Post-flowering drought tolerance was evaluated in 367 Sudanese sorghum lines using a fluorescence bioassay developed by scientists in the USDA Plant Stress and Germplasm Development Unit in Lubbock, Texas. Eight lines were initially selected for their stress tolerance. Additional studies led to the selection of three lines to move into the germplasm pipeline within the Cropping Systems Research Laboratory for future public release. These lines will provide new genetic resources for improved drought stress tolerance during grain fill. 02 High grain yield potential mutants and genes identified in sorghum. Over 30 independent sorghum multiseeded (msd) mutants were identified. The msd mutants have the potential to triple the seed number and double the seed weight per panicle as compared to the non-mutated BTx623. Two genes responsible for the trait have been identified. Perfect single nucleotide polymorphism (SNP) markers have been developed for marker- assisted introgression of this trait into elite sorghum lines. Over 400 advanced B & R selections have been advanced to the F4 stage for hybrid test. These achievements have the potential to significantly boost sorghum grain yield and may also lead to yield improvement in other cereals. 03 Cold tolerance evaluated for two sorghum recombinant inbred populations. For FY 2013-2014, studies on early season cold tolerance focused on completing the screening of a recombinant inbred population derived from BTx623 X NSL51071 (Population 3) for early season cold tolerance in the field and under controlled conditions. Further studies of genetic underpinnings of cold tolerance based on variation for different monosaccharide content of germinating seeds under cold stress were accomplished for the BTX623 * PI567946 (HKZ) population. In addition, germplasm from GRIN and Texas A&M University were evaluated in the spring of 2014 for cold germination and field vigor. A set of 60 elite materials was identified as cold tolerant and crossed with elite USDA breeding germplasm. These lines and characterization will aid the identification of seedling cold tolerance in sorghum.
Impacts
(N/A)
Publications
- Swapan, R., Abu, K., Hye-Rim, K., Soo-Jeong, K., Hee-Young, J., Jung-Hee, K., Jong-In, K., Tae-Seok, K., Xin, Z., Sun-Hee, W. 2014. Proteome profiling of seed from inbred and mutant line of sorghum (Sorghum bicolor). Australian Journal of Crop Science. 8(4):606-611.
- Narayanan, S., Aiken, R., Xin, Z., Prasad, V., Yu, J. 2014. A simple quantitative model to predict leaf area index in sorghum. Agronomy Journal. 106(1):219-226.
- Burow, G.B., Xin, Z., Burke, J.J., Hayes, C.M. 2014. Characterization of novel multi-seeded (msd) mutants of sorghum for increasing grain number. Crop Science. 54:1-8.
- Burow, G.B., Burke, J.J., Xin, Z. 2013. Developmental and genetic analysis of a short leaf mutant, a key resource for plant architecture modification in sorghum. Journal of Plant Growth Regulation. 71:271-280.
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