Progress 10/01/04 to 09/30/09
Outputs
OUTPUTS: Advanced yield trials were conducted in three locations in New Mexico and many locations across the Cotton Beltwide in 2009 on two Acala 1517 breeding lines with insect resistant BGII and herbicide resistant Roundup Ready Flex (RF) traits. Seed increase and large strip plot test for the two elite Acala 1517 BGII/RF lines were arranged in 2009, and their ginning and spinning properties are being evaluated in cooperation with USDA-ARS Southwest Cotton Ginning Lab. Based on incomplete results received and analyzed, one line outperformed or had similar yield as the conventional checks. For example, it was the highest yielding genotype of 31 entries including 29 were from seed companies tested in Clovis, NM. About 90 advanced breeding lines and 150 preliminary breeding lines derived from interspecific hybridization between Upland and Pima cotton were tested in eight different replicated field tests in 2009. It appears that some of them had significantly higher yield than 1517-99. Fiber quality testing is under way. A new breeding line NM03012 has been tested since 2003 in numerous environments and continued to perform very well in the 2009 tests. It is expected that it be released as a new conventional Acala 1517 cultivar in 2010. Seed increase and a strip plot test for this advanced breeding line were arranged in 2009 and its ginning and spinning properties are being evaluated. 146 backcrossed inbred breeding lines derived from Upland x Pima interspecific hybrids were evaluated under both normal and reduced irrigation conditions in the field for drought tolerance in Las Cruces and Artesia in 2009. Approximately 50 SSR markers were added to the population in 2009. The Acala 1517 BGII/RF lines and advanced conventional breeding lines were also evaluated in the field for Verticillium wilt resistance in Artesia in 2009. The results will lead to the identification of genes or quantitative trait loci (QTL) for drought and Verticillium resistance. Using microarray analysis and quantitative PCR, genes responsive to salt and drought stresses, semigamy, and male fertility restoration were identified and confirmed. Seed increase and a strip plot test for two Pima cotton lines were arranged in 2009. They have exhibited high yield potential with 10-20% higher yield than the check Pima S-7. The fiber quality of the two lines is similar or better, and their ginning and spinning properties are being evaluated. Additionally, in collaborating with Monsanto, 7 Pima cotton lines were backcrossed (at BC1F1 stage) for introducing BGII and RF genes into Pima cotton. PARTICIPANTS: Nothing significant to report during this reporting period. TARGET AUDIENCES: Nothing significant to report during this reporting period. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
Impact on New Mexico economy and environment New Mexico is a small cotton production state with many small cotton farms which are still growing saved Acala 1517 seed in 2009. However, the acreage of Acala 1517 was not officially collected. Impact on other breeding programs Based on the very recent information from seed companies, Acala cotton germplasm lines released recently from the program have been used by the private industry to have developed some very promising lines. These lines are expected to be released by seed companies for commercialization. The National Cotton Variety Testing (NCVT) Committee also requested a new Acala 1517 be considered as one of the national cotton variety standards for 2011-2013. Contributions to knowledge Numerous cotton germplasm lines were evaluated for Verticillium wit, drought and salt tolerance. This resulted in resistant/tolerant germplasm identified, laying a foundation for breeding, genetic, and genomic studies. We have developed a number of elite germplasm lines with desired fiber quality and high yield potential from interspecific breeding. This represents one of the first successful examples in cotton breeding in a century long attempt to significantly increase crop yield from interspecific hybridizations by introducing genes from one species to another. The Acala 1517 germplasm will continue to make substantial contributions to cotton breeding and industry in the U.S. A new marker system called promoter anchored amplified polymorphism (PAAP) was reported from the program, which will provide a means to profile sequence variations in promoter regions and to study their associations with agronomic traits. A number of DNA markers including SSCP, STS and CAP were developed and reported from fiber candidate genes. This will provide candidate markers to study their relationships with fiber yield and quality for marker-assisted selection. Several mitochondrial candidate genes associated with cytoplamic male sterility (CMS) were identified and reported. This represents the first work in investigating the molecular mechanism of CMS in cotton. Many drought and salt responsive genes have been identified and confirmed for the first time in cotton, which will provide a base for identifying genes responsible for abiotic stress tolerance and for developing candidate gene markers for stress tolerance breeding in cotton.
Publications
- Wang Fei, Chunda Feng, M. O'Connell, J. McD. Stewart, and Jinfa Zhang. 2009. RFLP analysis of mitochondrial DNA in two cytoplasmic male sterility systems (CMS-D2 and CMS-D8) of cotton. Euphytica (published online in Oct. 2009)
- Ulloa, M., R. Percy, Jinfa Zhang, R. B. Hutmacher, S. D. Wright and R. M. Davis. 2009. Registration of four Pima cotton germplasm lines having good levels of Fusarium wilt race 4 resistance with moderate yields and good fibers. J. Plant Registrations. 3: 198-202
- Lu Y., J. Curtiss, R. Percy, R. G. Cantrell, Shuxun Yu, E. Hughs and Jinfa Zhang. 2009. DNA polymorphisms of genes involved in fiber development in a selected set of cultivated tetraploid cotton. Crop Sci. 49: 1695-1704
- Wang Fei, Bing Yue, Jinguo Hu, J. McD. Stewart and Jinfa Zhang. 2009. A targeted region amplified polymorphism (TRAP) marker for fertility restorer gene Rf1 and chromosomal localization of Rf1 and Rf2 in cotton. Crop Sci. 49: 1602-1608
- Wang D. L., J. W. Yu, S. X. Yu, H. H. Zhai, S. L. Fan, M, Z, Song, and J. F. Zhang. 2009. The construction of a cDNA library from seed. Cotton Sci. 21: 351-355
- Yu J. W., S. X. Yu, J. F. Zhang, and H. H. Zhai. 2008. QTL mapping for fiber quality traits based on a dense genetic linkage map with SSR, TRAP, SRAP and AFLP markers in cultivated tetraploid cotton. Cotton Sci. 20:34
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Progress 01/01/08 to 12/31/08
Outputs
OUTPUTS: Advanced yield trials on insect resistant BGII and herbicide resistant Roundup Ready Flex (RF) Acala 1517 BGII/RF with Monsanto's second generation biotechnology traits were conducted in two locations in 2008 and several lines exhibited more than 10% higher yield than the insect resistant Bt cultivar Acala 1517-99W released in 2006. Seed increase for four of the elite Acala 1517 BGII/RF lines with good fiber quality was arranged in 2008 and their ginning and spinning properties are being evaluated before release as the replacement for Acala 1517-99W. About 90 advanced breeding lines and 90 preliminary breeding lines derived from interspecific hybridization between Upland and Pima cotton were tested in six different field tests in 2008. Many of the new breeding lines had 10-30% higher yield than 1517-99W. Fiber quality testing is under way. A small amount of seed increase for several advanced breeding lines was arranged in 2008 and their ginning and spinning properties are being evaluated. Acala 1517 cotton cultivars released from the New Mexico State University Cotton Breeding Program were compared in Mesilla Valley (Las Cruces), NM, in 2008 for fiber yield, yield component, quality, and growth characteristics. The more recently released cultivars tended to have higher growth rate. The trends in trait improvement will guild breeding strategies for the Acala cotton breeding program. 146 breeding lines derived from Upland x Pima interspecific hybrids were evaluated in the field for both drought (in Las Cruces and Artesia) and Verticillium wilt resistance (in Artesia) in 2008. The Acala 1517 BGII/RF lines were also evaluated in the field for Verticillium wilt resistance in Artesia in 2008. Using microarray analysis, a number of responsive genes to salt and drought stresses were identified and confirmed. One backcross inbred line population (BIL) of 146 lines was tested under both normal and reduced irrigation conditions in Las Cruces and Artesia, NM, in 2008. Approximately 550 markers were developed for the BIL population to identify desirable genes/QTL for yield, drought and Verticillium wilt tolerance, and quality. To facilitate fine mapping of genes/QTLs and select progeny for combined yield and fiber quality, more than 800 progeny rows derived from Upland x Pima hybrid were tested in 2008.Small amount of seed increase was made in 2008 for several Pima cotton lines. These lines have been field tested in Maricopa, AZ and Las Cruces in 2006 and 2007, and again tested in Las Cruces in 2008. They have exhibited high yield potential with 10-20% higher yield than Pima S-7. The fiber quality of these lines is similar or better and their ginning and spinning properties are being evaluated. Furthermore, with an agreement between NMSU and Monsanto under their Cotton States Program, 7 Pima lines were sent to Monsanto for introducing BGII and RF genes into the elite Pima lines. In collaboration with USDA-ARS in Maricopa, AZ and Shafer, CA, six Pima cotton germplasm lines were co-released. PARTICIPANTS: Nothing significant to report during this reporting period. TARGET AUDIENCES: Nothing significant to report during this reporting period. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
Based on the very recent information from seed companies, Acala cotton germplasm lines released recently from the program have been used by the private industry to have developed some very promising lines. These lines are expected to be released by seed companies for commercialization. Numerous cotton germplasm lines were evaluated for Verticillium wilt and salt tolerance. This resulted in resistant/tolerant germplasm identified, laying a foundation for breeding and genetic and genomic studies. We have developed a number of elite germplasm lines with desired fiber quality and high yield potential from interspecific breeding. This represents one of the first successful examples in cotton breeding in a century long attempt to significantly increase crop yield from interspecific hybridizations by introducing genes from one species to another. New markers were identified for two male fertility restorer genes in cotton. Based on several chromosome-anchored SSR markers, the two restorer genes (Rf1 and Rf2) were localized on chromosome D5 and anchored in a 13.6 cM region by two PPR gene-based markers, providing an incentive for further investigations of this chromosomal region containing Rf1/Rf2. The results also provide the base for map-based cloning of the restorer genes. We developed several DNA markers for root-knot nematode resistance, which can be used for marker-assisted selection in breeding to facilitate breeding for resistant cultivars. We constructed a high density linkage map with more than 1,000 DNA markers, which can be used for identifying desirable genes for cotton yield and fiber quality. Many drought and salt responsive genes have been identified for the first time in cotton, which will provide a base for identifying genes responsible for abiotic stress tolerance and for developing candidate gene markers for stress tolerance breeding in cotton.
Publications
- Pang M. X., R.G. Percy, S. H. Hughs, and Jinfa Zhang. 2008. Promoter anchored amplified polymorphism based on random amplified polymorphic DNA analysis (PAAP-RAPD) in cotton. Euphytica (online)
- Lu Y., J. Curtiss, D. N. Miranda, E. Hughs and Jinfa Zhang. 2008. ATG anchored AFLP (ATG-AFLP) analysis in cotton. Plant Cell Reports 27: 1645-1653
- Esmail R. M., J. F. Zhang, and A. M. Abdel-Hamid. 2008. Genetic diversity in elite cotton germplasm lines using field and RAPD markers. World J. Agric. Sci. 4: 369-375
- USDA-ARS and NMSU. 2008. Registration of PSI 113 and PSI 425 germplasm lines of Pima cotton possessing superior fiber quality traits.
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Progress 01/01/07 to 12/31/07
Outputs
1) Development of Acala 1517 Bt and Roundup-Ready (RR) cultivars: Several Acala Bt and Roundup Ready lines were tested in three locations in New Mexico and multiple locations across the Cotton Belt in 2007. Advanced yield trials on Acala 1517 BGII/RF with Monsanto's second generation biotechnology traits were conducted in two locations in 2007 and several lines displayed equal or better yield potential than Acala 1517-99W. One of the elite lines will be tested for two more years and selected for release as the replacement for Acala 1517-99W. Acala 1517-99W was the first insect resistant Bt cotton cultivar released from the public sector in the U.S. After its release in early 2005, Acala 1517-99W was planted to 13.4% and 6.8% cotton acreage in New Mexico in 2006 and 2007, respectively. 2) Conventional Acala 1517 Germplasm Development: More than 90 advanced breeding lines derived from interspecific hybridization between Upland and Pima cotton were tested in two locations
in 2007, some of which had 7-18% higher yield than 1517-99W. Many breeding lines also exhibited improved fiber quality. 3) Genetic and genomics research to identify and utilize desirable genes for yield, quality, root-knot nematode and Verticillium wilt resistance, and drought and heat tolerance. Comparative field performance of Acala 1517 cultivars released since the 1930s Acala 1517 cotton cultivars released from the New Mexico State University Cotton Breeding Program and other Acala cotton cultivars mainly released from California were compared in Mesilla Valley (Las Cruces) and Pecos Valley (Artesia), NM, in 2005, 2006 and 2007 for fiber yield, yield component, quality, and Verticillium wilt resistance. The trends in trait improvement will guild breeding strategies for the Acala cotton breeding program. 4) Verticillium wilt resistance and salt tolerance in cotton: germplasm evaluation and inheritance: Since 2003, 267 cultivars and germplasm lines were screened for Verticillium
wilt resistance in the greenhouse, while 357 cultivars and germplasm lines were screened in the field. Based on the segregation analysis, 1-2 genes resistant to Verticillium wilt were identified in two F2 populations made from Upland x Pima crosses. Since 2005, more than 200 gernplasm lines were evaluated for salt tolerance in the greenhouse. Many genotypes with high level of resistance or tolerance have been identified for further studies in cotton breeding and genetics. Population development and identification of genes/quantitative trait loci (QTL) One backcross inbred line population (BIL) of 146 lines was tested under recommended crop production managements in Las Cruces, NM and Maricopa, AZ in 2005, 2006 and 2007. Approximately 500 markers were developed for the BIL population to identify desirable genes/QTL for yield and quality. To facilitate fine mapping of genes/QTLs, more than 1,500 advanced F5:F6 progeny rows as single plant selections from 294 F4:F5 progenies of Acala
1517-99 x Pima Phy 76 were tested in Las Cruces, NM in 2007. This will create one of the largest recombinant inbred line (RIL) populations for high resolution mapping of fiber yield and quality genes in cotton.
Impacts
Impact on New Mexico economy and environment: We developed and released the first public transgenic Bt (insect resistant) cotton cultivar (1517-99W) in the United States in 2005. It was grown in more than 13% (8,417 acres) and 6.8% (3400 acres) of cotton acreage in New Mexico in 2006 and 2007, respectively, according to the "2006-2007 Variety Planted" and "2007-2008 Variety Planted" reported by USDA-AMS. The new cultivar 1517-99W increased cotton production by 70-140 pounds per acre, totaling >600,000-1,200,000 pounds ($300,000-600,000) and 238,000-476,000 pounds ($150,000-300,000) of cotton in increase for New Mexico in 2006 and 2007, respectively. This new insect resistant Acala 1517 cultivar with insect resistance also is expected to reduce production cost and chemical contamination by reducing the use of pesticides. Impact on other breeding programs: Based on the very recent information from seed companies, Acala cotton germplasm lines released recently from the
program have been used by the private industry to have developed some very promising lines. These lines are expected to be released by seed companies for commercialization. Contributions to knowledge: Numerous cotton germplasm lines were evaluated for Verticillium wit and salt tolerance. This resulted in resistant/tolerant germplasm identified, laying a foundation for breeding and genetic and genomic studies. We have developed a number of elite germplasm lines with desired fiber quality and high yield potential from interspecific breeding. This represents one of the first successful examples in cotton breeding in an attempt to significantly increase crop yield from interspecific hybridizations by introducing genes from one species to another. New markers were identified for a male fertility restorer gene in cotton, providing the base for map-based cloning of the restorer gene. We developed several DNA markers for root-knot nematode resistance, which can be used for marker-assisted
selection in breeding to facilitate breeding for resistant cultivars. We constructed a high density linkage map with more than 1000 DNA markers, which can be used for identifying desirable genes for cotton yield and fiber quality.
Publications
- Zhang Jinfa, R. B. Turley and J. McD. Stewart. 2007. Comparative analysis of gene expression between CMS-D8 restored plants and normal non-restoring fertile plants in cotton by differential display. Plant Cell Reports (Online Dec. 2007)
- Wang Fei, J. McD. Stewart and Jinfa Zhang. 2007. Molecular markers linked to the Rf2 fertility restorer gene in cotton. Genome 50: 818-824
- Niu C., Doug J. Hinchliffe, Yingzhi Lu, Roy G. Cantrell, C. Wang, Philip Roberts and Jinfa Zhang. 2007. Identification of molecular markers linked to root-knot nematode resistance in cotton (Gossypium hirsutum L.). Crop Sci. 47: 951-960
- Yu Jiwen, Yu Shuxun, Lu Cairui, Wang Wu, Fan Shuli, Song Meizhen, Lin Zhongxu, Zhang Xianlong and Jinfa Zhang. 2007. A high-density linkage map of cultivated allotertrapoid cotton based on SSR, TRAP, SRAP and AFLP markers. J. Integrated Plant Biol. 49: 716-724
- Zhang Jinfa, Yuan Y., C. Niu, Doug J. Hinchliffe, Y. Lu, Shuxun Yu, R. G. Percy and R. G. Cantrell. 2007. AFLP-RGA markers in comparison with RGA and AFLP in cultivated tetraploid cotton. Crop Sci. 47: 180-187
- Zhang J. F., C. Waddell, C. Sengupta-Gopalan, C. Potenza and R. G. Cantrell. 2007. Diallel analysis of root-knot nematode resistance based on galling index in upland cotton. Plant Breed. 126: 164-168
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Progress 01/01/06 to 12/31/06
Outputs
Advanced yield trials on Acala 1517 Bt, RR, and Bt/RR were conducted in 2006. After its release in early 2005, Acala 1517-99W was planted to 8,500 acres in New Mexico in 2006. This accounted for 13.4% acreage of Upland cotton grown in New Mexico this year. Some conventional Acala 1517 germplasm lines continued to show a significant yield improvement (5-30%) over 1517-99. Many breeding lines also exhibited improved fiber quality. Six high-yielding and high fiber quality germplasm lines will be suggested to be released.
Impacts
We developed and released the first public transgenic Bt (insect resistant) cotton cultivar (1517-99W) in the United States in 2005 which was grown in more than 13% (8,417 acres) of cotton acreage in New Mexico in 2006, according to the "2006-2007 Variety Planted" report by USDA. The new cultivar 1517-99W increased cotton production by 70-140 pounds per acre, totaling >600,000-1,200,000 pounds ($300,000-600,000) in increase for New Mexico in 2006 alone. The figure is expected to increase substantially in the years to come. Recently, New Mexico growers reported more than 3 bales (>1,440 pounds) per acre production from growing Acala 1517-99W in 2006. This translated to 25,251 bales (12,120,480 pounds) cotton fiber production by 1517-99W, totaling >$6 millions gross income for New Mexico cotton growers. We are targeting ~50% acreage coverage by our new Acala 1517 cotton cultivars including this one (1517-99W) in our state in the next several years. Therefore, the
economic impact of this cotton breeding program will soon be >$25 millions for our state.
Publications
- R. G. Percy, Jinfa Zhang, and R. G. Cantrell. 2006. Genetic variation for agronomic and fiber properties in an introgressed recombinant inbred population of cotton. Crop Sci.: 1311-1317
- Zhang Jinfa, C. Waddell, C. Sengupta-Gopalan, C. Potenza and R. G. Cantrell. 2006. Relationships between root-knot nematode resistance and plant growth in Upland cotton: galling index as a criterion. Crop Sci.: 1581-1586
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Progress 01/01/05 to 12/31/05
Outputs
Advanced yield trials on Acala 1517 Bt, RR, and Bt/RR were conducted from 2003-2005. The first Bt cultivar Acala 1517W was released early 2005, which has 10% yield advantage over the current Acala cultivar, 1517-99. Acala 1517-99W was licensed to Dow AgroScience for commercialization in 2005. Approximately 20,000 pounds of 1517-99W seed was produced in 2003 in Charlie Tharp Farm and sold out by Helena Chemical Co. in 2005. Approximately 150,000 pounds of 1517-99W were produced in 2005 that is expected for more than 10,000 acres of cotton production in 2006. Some promising Acala 1517 Bt lines showed 10-40% yield improvement. One Acala 1517 RR and one Acala Bt/RR stack cultivar are expected to be released in 2006. These cultivars represent the first transgenic cotton cultivars developed and released from the public sector in the U.S. Growing the Bt Acala cotton will eliminate pesticide use for pink bollworm control. Some conventional Acala 1517 germplasm lines showed a
significant yield improvement (5-30%) over 1517-99. Many breeding lines also showed improved fiber quality. Three high-yielding germplasm lines (1517-02, 1517-03, and 1517-04) and several high fiber strength germplasm were suggested to be released. One breeding line will be released as a commercial cultivar in 2006. 98 recombinant inbred lines (RIL) were developed from a cross between TM-1, the genetic standard of upland cotton, and NM 24016, an Acala breeding line with substantial germplasm introgression from Pima cotton. The RIL lines, together with their parents were field tested in replicated trials in Las Cruces, NM and Maricopa, AZ in 2001 and 2002. Boll size, lint percentage, lint yield, and fiber quality traits were measured. A linkage map comprising of 23 linkage groups with 177 DNA markers was constructed. The majority of the markers were AFLP and SSR. Included were also other markers such as RFLP, RAPD, SRAP and STS. Using Mendelian genetics, F2 populations from crosses
with Auburn 634 and its derived resistant line M-240 indicated that root-knot nematode resistance in Auburn 634 is either controlled by one dominant gene or one dominant gene and one recessive gene. By comparing pairs of near isogenic lines (NIL) with or without the Auburn source of resistance, two RGA, two RAPD, and two AFLP markers were identified to be consistently polymorphic between the NIL. The two RAPD markers and one of their converted STS markers classified 23 resistant and 8 susceptible germplasm into three groups that reflected their resistance origins. To determine their utility for marker-assisted selection of nematode resistance in cotton, these RKN resistance-associated markers were screened to test linkage to resistance loci using progenies segregating for the resistance of Auburn source. One RAPD marker and its converted sequence tagged site (STS) marker were tightly linked to the CAP marker associated with the NemX resistance. We have also isolated 165 disease
resistance gene analogues (RGA) and mapped more than 200 RGA markers to 28 cotton chromosomes/linkage groups.
Impacts
Due to their lower yield, Acala 1517 cultivars are now only planted in less than 10% cotton average in New Mexico even though its fiber price is estimated to be $0.06 higher than other Upland cottons. If new competitive high yielding Acala 1517 cultivars can be grown in 50% of the cotton acreage, New Mexico cotton farmers can increase their profitability by $2 million per year. New Acala 1517 cultivars with insect, nematode, disease and herbicide resistance can also reduce production cost and environmental contamination of pesticides. The markers that are associated with root-knot nematode resistance and agronomic traits will be very useful in facilitating marker-assisted selections in cotton breeding.
Publications
- Zhang Jinfa, Yingzhi Lu, R. G. Cantrell, and E. Hughs. 2005. Molecular marker diversity and field performance in commercial cotton cultivars evaluated in the southwest USA. Crop Sci. 45:1483-1490
- Zhang Jinfa, Y. Lu, H. Adragna, and E. Hughs. 2005. Genetic improvement of New Mexico Acala cotton germplasm and their genetic diversity. Crop Sci. 45: 2363-2373
- Zhang Jinfa, Yingzhi Lu, and Shuxun Yu. 2005. Cleaved AFLP (cAFLP), a modified amplified fragment length polymorphism analysis for cotton. Theor. Appl. Genet. 111: 1385-1395
- Zhang Jinfa, J. McD. Stewart and T. H. Wang. 2005. Linkage analysis between gametophytic restorer Rf2 gene and genetic markers in cotton. Crop Sci. 45:147-156
- Feng C.D., Zhang Jinfa and J. McD. Stewart. 2005. Development of STS markers associated with cotton CMS fertility restorer gene Rf1. Theor. Appl. Genet. 110:237-243
- Hinchliffe, D., Carol Potenza, Champa-Segupta Gopalan, R. G. Cantrell and Jinfa Zhang. 2005. Resistance gene analogues (RGAs) are mapped on homoeologous chromosomes in cultivated tetraploid cotton. Theor. Appl. Genet. 110: 237-243
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