Source: UNIVERSITY OF FLORIDA submitted to
ADVANCING HARVEST INDEX IN WHEAT THROUGH GENOMIC ENABLED PHYSIOLOGICAL BREEDING
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
EXTENDED
Funding Source
Reporting Frequency
Annual
Accession No.
1011251
Grant No.
2017-67007-25929
Project No.
FLA-AGR-005549
Proposal No.
2016-06700
Multistate No.
(N/A)
Program Code
A1142
Project Start Date
Dec 1, 2016
Project End Date
Nov 30, 2018
Grant Year
2018
Project Director
Babar, M. A.
Recipient Organization
UNIVERSITY OF FLORIDA
G022 MCCARTY HALL
GAINESVILLE,FL 32611
Performing Department
Agronomy
Non Technical Summary
Wheat is one of the three most important cereal crops globally and is grown in more than 218 million ha of land with an average grain yield of 3.27 t ha-1. Yields of wheat must be doubled in the next 30 years to avert a major food crisis . Research to enhance wheat photosynthesis may facilitate improvement of potential biomass, but yield benefits may be small unless 'useful', as against 'non useful', biomass can be discriminated and maximized. Harvest index (HI, grain dry matter (DM) yield / aboveground DM) has a hypothetical limit of 65% in wheat and also there has been no significant progress in its maximum expression of HI from post Green Revolution values of ca. 45-51% in spring wheat and 50-55% in winter wheat. Recent yield improvement of CIMMYT spring wheats in the Yaqui Valley (North-West Mexico) has been associated with increased aboveground biomass and grain weight, but also with increased plant height and decreased HI. Furthermore, the expression of HI in this range is unpredictable in both the genetic and environmental context. Stable expression of HI at values of 55% and abovewould deliver a step change (~20%) in yield potential (given that the average expression is closer to 45%), however, a limited understanding of its genetic basis restricts the ability to improve HI. Overwhelming evidence suggests that during grain filling wheat yield potential is sink-limited (grain number per spike and unit area), as carbon accumulation is limited by the storage capacity of the grains Therefore, strategies to improve grain number per unit area are one of the most important avenues in the genetic improvement of HI and yield potential.Our long-term goal is to develop an ideal ideotype with HI ≥ 60% by combining increased spike partitioning, fruiting efficiency, fertile florets per spikelet, and improved spike morphology. The specific objectives are to develop new breeder-friendly molecular markers for grain partitioning traits that permit photosynthetic products to be consistently translated to grain yield, screen genetic resources determining grain partitioning in high biomass backgrounds, identify mechanisms determining grain partitioning traits, and design ideal plant ideotypes for high HI and yield. We will achieve our goals by: 1) characterizing two association panels, CIMMYT spring wheat and US soft wheat, for photosynthetic capacity, HI, grain yield and grain partitioning traits, including spike partitioning fruiting efficiency and their determinants stem internode and lemma partitioning and rachis specific weight, 2) genetic characterization of the panels using genotype by sequence-SNP markers, and validated them in bi-parental populations after converting them into KASP-SNPs 3) screening wider resources for better understanding of the range of potential alleles influencing these grain traits and interactions with environments 4) designing ideotypes and establishing pre-breeding crosses. Successful identification of association between alleles and grain partitioning traits will help to understand the mechanism of yield improvement and deliver a significant impact on yield improvement
Animal Health Component
0%
Research Effort Categories
Basic
25%
Applied
75%
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
20115491081100%
Goals / Objectives
Goals / ObjectivesThis proposed project will be focused on developing the best ideotypes that can maximize conversion of enhanced carbon capture and biomass growth to grain through exploration of new genetic variation for related traits and genetic markers associated with these traits. Increasing HI in wheat from the current value of ca. 0.48 to 0.60 will increase yield by -25%. The major goals of this proposal are:Develop new breeder-friendly molecular markers for grain partitioning traits that permit photosynthesis products to be consistently translated to grain yield through genome-wide association study (GWAS) using two association panels in high biomass backgrounds, one panel comprising of US southern, eastern, and southeastern facultative soft wheats, and one CIMMYT spring wheatsScreen diverse sets of genetic resources including CIMMYT primary synthetic lines and US soft wheats for markers for grain traits determining grain partitioning in high biomass backgrounds.Identify mechanisms determining grain partitioning traits and genotype-by-environment interaction through physiological dissection of subsets of wheat genotypes.Design ideal plant ideotypes and establish pre-breeding crosses in the USA and CIMMYT wheat breeding programs.
Project Methods
Objective 1. Develop new molecular markers for grain traitsTwo association panels will be characterized for physiological traits that determine spike partitioning, fertile floret number and redistribution of carbon to the grain, fruiting efficiency, HI and grain yield with one panel at UFL, Gainesville and another panel at the CIMMYT IWYP Hub, Ciudad Obregon. The US panel is comprised of 248 US soft red facultative wheat genotypes, while the CIMMYT IWYP Hub panel is High Biomass Association Panel (HiBAP) comprised of 150 spring lines at the respective sites in 2016-7 and 2017-8. The plots will be grown under fully irrigated conditions. Wheat panels will be genotyped using genotyping-by-sequencing (GBS) markers and genomic regions associated with the traits of interest will be determined. GBS-SNP markers will be converted to KASP markers and validated in four biparental doubled-haploid mapping populations owned by UFL. For each QTL identified from GWAS, 2-3 KASP markers will be developed, their haplotypes will be determined and validated in at least one linkage mapping population. Analysis of marker-trait associations will be done after comparing several models that account for population structure and familial relatedness using the unified mixed model using TASSEL and R software. We will identify genetic markers associated with key grain partitioning traits including spike partitioning index, fruiting efficiency, grain number and HI.Objective 2. Screen wider resources: CIMMYT exotic and US wheat panelsThe panels of wider germplasm will be genotyped for haplotypic variation for the markers identification and will provide a better understanding of the range of potential loci and alleles that influence these grain traits and interactions with the environment and in terms of epistasis. The panels of wider germplasm will comprise:CIMMYT Exotic Panel (CExP), Primary Synthetics Diversity panel (n=160), Bread wheat diversity panel, and 7Ag.7DL translocation lines panelUS soft wheat panel. This panel will constitute a different set of newly developed wheat breeding lines (around 400) from different soft red wheat and spring wheat breeding programs in the USA.Phenotypic evaluation of the target grain partitioning traits in Objective 1 will be used to screen the two new panels in year 3. The phenotyping measurements will include phenology, rapid screening methods for aboveground biomass at anthesis, spike partitioning index at GS65 and fruiting efficiency, plant height (and stem internode lengths) at harvest, grain yield, HI, and yield components.Objective 3. Identify mechanisms determining grain traits and quantify genotype-by-environment interactionPhysiological characterization of a subset of the two panelsA set of 20 genotypes (10 representative lines of each of the HiBAP and US association panels) will be used as common checks for the two association panels. A more detailed set of physiological measurements will be carried out on these 20 genotypes at both UFL and IWYP hub to identify the mechanisms determining the grain sink traits and to quantify G x E and the heritability of the traits. The measurements that will be carried out at UFL and IWYP hub are those outlined in Objective 1 plus measurements to quantify stem structural internode partitioning, spike morphological components, and photosynthetic capacity including stem structural and soluble DM in internode 1 (peduncle), internode 2, internode 3 and internode 4+ at GS65, spike partitioning at harvest (awns, rachis, glume, palea, lemma), stem water soluble carbohydrate, and photosynthetic capacityPlant hormone profiling of a HiBAP subset at UoNA subset of 10 genotypes from the CIMMYT HiBAP panel contrasting for fruiting efficiency and grain number will be selected based on year 1 results. These 10 genotypes will be assessed in a glasshouse experiment at UoN in each of 2017 and 2018 for fruiting efficiency, grain number and plant growth regulator profiles (including cytokinin and abscisic acid; four replicates per genotype). Hormone profiling will be carried out by ultra-performance liquid chromatography-electrospray ionization-tandem mass spectrometry. The trait phenotyping related to fruiting efficiency (grains per unit spike DM at anthesis) in the project is focused mainly onspike morphological partitioning in the two association panels, but we consider the integration of hormone profiling on a small subset of germplasm could provide added value to the project. In particular, we consider it may be useful to test the hypothesis increased FE is associated with cytokinin levels in spikes influencing floret survival (proportion of floret primordia that reach the stage of fertile florets at anthesis). For example, the cloning of a major QTL Gn1a for rice grain number regulating cytokinin oxidase/dehydrogenase (CKX) - reduced expression of this gene leading to accumulation of cytokinin in inflorescence meristems and higher grain number - illustrates how such studies can lead to theidentification of candidate genes and markers for use in breeding programs (Ashikari et al., 2005, Science 309, 741-745). Plant hormone signalling may also mediate responses to temporary environmental stresses during the rapid spike growth phase preanthesis which impact on grain number; e.g. Davies et al. (2002, New Phytologist 153, 449-460) (water/ABA) and Hays et al. (2007, Plant Science 172, 1113-1123) (temperature/ethylene). We consider the results for the subset of germplasm could provide the basis for future GWAS analysis for these plant signalling traits.Objective 4. Design ideotypes and establish pre-breeding crosses at UFL and CIMMYTIn year 3, a quantitative crop design approach will be used to identify the optimum combination of traits for maximizing HI and yield. The most promising lines (20 crosses per panel) will be crossed at UFL and CIMMYT in year 3. This will feed directly into the ongoing pre-breeding programs initiated at UFL and CIMMYT to increase yield potential and to which any relevant technologies developed during the project will also be applied. Those genotypes from the various genetic resources that outperform checks will be channeled into pre-breeding programs at UFL and CIMMYT in year 3.Project management plan: Ali Babar (PI) will perform the day to day management of the project and dealing with reports. PI and Post-doc will be also responsible for planning of experiment, data taking (phenotypic characterization of US association panel, elite set of wheat lines, and the detailed characterization of subset of the association panel, local data management and analysis at UF. Co-PI Guihua Bai and graduate/post-doc will lead marker analysis and validation, and will communicate with other project personnel. Co-PI Foulkes and graduate student will be responsible for planning, data taking, hormone analysis, etc in UoN. Co-PI Matthew Reynolds at CIMMYT will be responsible for supervising graduate student from UoN on phenotyping characterization on the CIMMYT HiBAP panel, Exotic Panel, and the detailed characterization of the HiBAP subset at CIMMYT-IWYP. Co-PI Sivakumar Sukumaran will lead the effort of overall data and GWAS analysis, etc. He will also be responsible for data management in IWYP platform hosted at CIMMYT. One Steering Group meeting will be held per year. The PIs from each institute will hold quarterly meetings by videoconferencing. Short quarterly and longer yearly reports will be provided to NIFA and IWYP.Data management plan: We will generate data associated with phenotype and genotype. All data generated from this project will be housed, and the maintenance and manipulation of raw data and metadata will be dealt with IWYP platform "Germinate" hosted at CIMMYT. PI and all Co-PIs will get access to the IWYP platform. In addition, as a back-up we will store metadata at UFL "Microsoft SQL server". The post-doc will be responsible for managing data at UFL.

Progress 12/01/16 to 11/30/17

Outputs
Target Audience:Global wheat research community including wheat breeding and genetics program in the USA. Academic and research community of US and around the world. Representative for food industry globally. Agricultural extenion personnell within USA and globally. Changes/Problems:No major changes in objectives, goals, and research approaches anticipated for 2017-18. What opportunities for training and professional development has the project provided?Bethany Love (PhD student registered Nottingham University) started on the project on August 2017. She will carry out the glasshouse experiments at Nottingham and contribute to the phenotyping of the HiBAP population and wider germplasm and associated GWAS analysis under Objectives 1-3 as outlined in the proposal. Dr. Jia Guo is newly appointed post-doc at University of Florida and is responsible for phenotyping of US soft wheat association panel at two locations in Florida. In addition, Dr. Guo will phenotype two double haploid population for marker conversion and validation, haplotype analysis and introgression of QTLs in different genetic background at UF. Dipendra Shahi is a Ph.D. student started on the project from Nov of 2016. He is full time on the project for phenotyping of association panel. Dipendra is funded through University of Florida. His responsibility is aligned with objectives 1 and 3 in the proposal. Student assistant Abdul Halim and Smita Rayamajhi were also trained through the project at UF. How have the results been disseminated to communities of interest?The results of 2016-17 WIll be presented at PAG meeting at San Diego and IWYP project directors meeting in 2018. What do you plan to do during the next reporting period to accomplish the goals?Objective 1 Develop new breeder-friendly molecular markers for grain partitioning traits (GWAS) At the CIMMYT IWYP Hub the HiBAP wil be phenotyped in 2017-8. While US soft wheat will be phenotyped at PSREU and NFREC, Florida. The core phenotyping measurements will include: i) phenology, ii) growth and partitioning at anthesis and iii) yield and yield components. Analysis of marker-trait associations will be carried out using TASSEL and R software (GAPIT package). For each QTL identified through GWAS analysis, 2-3 KASP markers will be developed, their haplotypes will be determined and validated in at least one linkage mapping population, and the validated KASP markers will be used for selecting the target QTL regions in breeding and for pyramiding the QTLs for grain traits through marker-assisted selection. Dr. Guihua Bai will lead breeder friendly KASP marker development. Dr. Babar and post-doc Dr. Jia Guo will be responsible for phenotyping of two double haploid populations at Florida for marker conversion and validation. The core phenotyping measurements will include: i) phenology, ii) growth and partitioning at anthesis and iii) yield and yield components. Objective 2. Screen wider resources: CIMMYT exotic panel and US soft and hard wheat panel Wider germplasmwill be screened at the CIMMYT IWYP Hub to gain a better understanding of the range of potential loci and alleles that influence these grain traits and interactions with the environment and in terms of epistasis. The panel of wider germplasm will comprise selected genotypes of three other CIMMYT panels: a) Primary Synthetics Diversity panel (n=160). b) Bread wheat diversity panel (n=370). c) 7Ag.7DL translocation lines panel. The core phenotyping measurements will include: i) phenology, ii) growth and partitioning at anthesis and iii) yield and yield components. Objective 3. Identify mechanisms determining grain traits and quantify genotype-by-environment interaction A set of 20 genotypes (10 representative lines of each of the HiBAP and US association panels) will be used as common checks for the two association panels in Objective 1. A more detailed set of physiological measurements will be carried out on these 20 genotypes at both UFL and IWYP hub to identify the mechanisms determining the grain sink traits and to quantify G x E and the heritability of the traits. The measurements will include: Growth and partitioning: Stem structural and soluble DM in internode 1 (peduncle), internode 2, internode 3 and internode 4+ at GS65 Spike partitioning at harvest (awns, rachis, glume, palea, lemma). Stem water soluble carbohydrate % at harvest. Photosynthetic capacity: Flag-leaf stomatal conductance weekly measured from GS51 to mid-senescence (GS75) The subset of 10 genotypes from the CIMMYT HiBAP will be assessed in a glasshouse experiment at UoN in 2017-8 for fruiting efficiency, grain number and plant growth regulator profiles. These results will also provide the basis for future GWAS analysis for these plant signalling traits.

Impacts
What was accomplished under these goals? Objective 1): Develop new breeder-friendly molecular markers for grain partitioning traits that permit photosynthesis products to be consistently translated to grain yield through genome-wide association study (GWAS) using two association panels in high biomass backgrounds, one panel comprising of US southern, eastern, and southeastern facultative soft wheats, and one CIMMYT spring wheats Two association panels (one panel at UFL, Gainesville and another panel at the CIMMYT IWYP Hub, Ciudad Obregon) were characterized for physiological traits that determine spike, lamina, and stem partitioning, fruiting efficiency, HI, above ground biomass, and grain yield. At UFL, the panel is comprised of 248 US soft red facultative wheat genotypes developed by different public and private wheat breeding programs. The panel was planted at Plant Science Research and Education Unit (PSREU), Citra, FL and North Florida Research and Education Center (NFREC), Quincy, FL for phenotypic characterization, The High Biomass Association Panel (HiBAP) was characterized at the CIMMYT IWYP Hub at Obregon, Mexico. The HiBAP panel comprised of 150 spring lines has been assembled by systematic screening of: (i) recent CIMMYT international bread wheat nurseries targeted to high yield environments, (ii) outstanding pre-breeding lines crossed and selected for high yield and biomass, and (iii) elite synthetic-derived lines. The HiBAP (High Biomass Association Panel) panel with high biomass was sown on 2 November 2016, in an alpha-lattice design with 4 replicates, at the International Maize and Wheat Improvement Center (CIMMYT) experimental station Norman E. Borlaug located in Yaqui Valley in Mexico. Physiological traits were measured at anthesis (GS65) +7d, when a full DM partitioning analysis was carried out (spike, leaf lamina and stem and leaf sheath DM proportions) including stem internode lengths: internode 2 and 3 (peduncle -1 and -2, respectively). At harvest, machine harvested yield, HI and yield components were assessed. The same traits were measured for US soft wheat panel at two locations (NFREC and PSREU) at anthesis+7d. Soft wheat panel was planted in a modified augmented design using three commercial varieties as repeated checks. HiBAP panel: Overall yields that ranged from 437 to 618 g m-2 (P<0.001) and above-ground biomass from 1123 to 1552 g m-2 (P< 0.001). Results showed genetic variation in most of the partitioning traits measured at GS65+7d and physiological maturity. Strong relations were found amongst genotypes between grain yield and AGDM (r =0.46, P< 0.001) and HI (r = 0.35, P< 001). There was strong a trade-off between AGDM and HI (r = -0.57, P<0.001) There was an association between enhanced grains m-2 and reduced length of true-stem internode 3 (peduncle -2) (r = -0.29, P<0.01) at anthesis (GS65 +7d) and reduced length of true-stem internode 2 (peduncle -1) (r = -0.32; P<0.01). Internode 2 and 3 lengths were also negatively associated with SPI (P< 0.001; Fig.1a) There was a positive linear association between fruiting efficiency (grain per unit spike DM at GS65+7d; FE) and grains m-2 (r = 0.46, P<0.001). Considering the partitioning indices at GS65+7d, there was a strong negative linear association between spike PI and stem PI (R2 = -0.58, P< 0.001) but a weak negative association between spike PI and lamina PI (R2 = -0.04; P< 0.05). US Soft wheat panel: Gneotypes showed significant genetic variations for grain yield(P<0.001) and for above-ground biomassm-2 (P< 0.001). Results showed genetic variation in most of the partitioning traits measured at GS65+7d and physiological maturity. Strong relations were found amongst genotypes between grain yield and AGDM (r =0.35***) and HI (r = 0.64***). There was signififcant trade-off between AGDM and HI (r = -0.21**). There was an association between enhanced grains m-2 and reduced length of true-stem internode 3 (peduncle -2) (r = -0.23**) at anthesis (GS65 +7d) . Spike partitioning index was strongly associated with grain yield (0.23**), HI (0.30***) and grains m-2 (0.25**). There was a positive linear association between fruiting efficiency and grains m-2 (r = 0.49***) and with harvest index (0.402***). Considering the partitioning indices at GS65+7d, there was a strong negative association between spike PI and stem PI (R2 = 0.42***) and between spike PI and lamina PI (R2 = 0.29***). These preliminary results suggest that genotypes with a longer internode 2 and 3 compete more with the spike for assimilate at GS65+7d and this is related to decreased Spike PI, grain number per unit area and HI. The genotyping of both panel is in progress by using the GBS (US soft wheat panel) and exom capture (CIMMYT HiBAP panel).The genotyping data will be used to identify QTLs for different traits. The genotyping information will be used for GWAS analysis. Genetic data will be analyzed using the TASSEL 5 software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium (GWAS). The genotyping of both panel is in progress and expected to completed by end of October. SNPs identified from Exon Capture and GBS that link to these QTLs will be converted into breeder-friendly KASP markers for breeding. Objective 2: Screen diverse sets of genetic resources including CIMMYT primary synthetic lines and US soft wheats for markers for grain traits determining grain partitioning in high biomass backgrounds. Wider germplasmwill be screened at the CIMMYT IWYP Hub to gain a better understanding of the range of potential loci and alleles that influence these grain traits and interactions with the environment and in terms of epistasis in 2017-18. The core phenotyping measurements will include: i) phenology, ii) growth and partitioning at anthesis and iii) yield and yield components. Objective 3): Identify mechanisms determining grain partitioning traits and genotype-by-environment interaction through physiological dissection of subsets of wheat genotypes. A more detailed analysis was carried out on a subset of 30 genotypes in the HiBAP and 10 genotypes in the US soft wheat panel for true-stem (TS) and leaf-sheath (LS) internode DM partitioning (peduncle, internode 2 and internode 3) and spike morphological DM partitioning (glume, palea, lemma, awns and rachis) at GS65+7d.Genetic variation among genotypes was found for true stem (TS) and leaf sheath (LS) DM partitioning indices at each internode (internode PI) with a strong negative association between Spike PI and true-stem internode 3 PI.Genetic variation was found for all spike component partitioning indices (spike component DM/total spike DM, excluding grain) (P< 0.05). There were negative linear associations between FE and DM partitioning to each component (glumes, lemma, palea, awns PIs). This likely reflected that overall smaller spikes and spike growth was associated with higher FE. The strongest trade-off appeared to be between FE with lemma PI.Seed for a subset of 10 HiBAP lines has been sent to University of Nottingham and a glasshouse experiment is currently ongoing at Nottingham to investigate genetic variation in grain number and fruiting efficiency and associations with plant growth regulator profiles. 4) Design ideal plant ideotypes and establish pre-breeding crosses in the USA and CIMMYT wheat breeding programs. This research will be conducted at year 2018-19.

Publications

  • Type: Journal Articles Status: Published Year Published: 2017 Citation: 1. C. Li, C. Li, B. F. Carver, R. Bowden, Z. Su, Z. Wang, and G. Bai. 2017. Mapping of Quantitative Trait Loci for Leaf Rust Resistance in the Wheat Population Ning7840 � Clark. Plant Dis. https://doi.org/10.1094/PDIS-12-16-1743-RE 2. Y. Lu, R. L. Bowden, G. Zhang, X. Xu, A. K. Fritz, and G. Bai. 2017. Quantitative Trait Loci for Slow-Rusting Resistance to Leaf 1 Rust in Doubled Haploid Wheat Population CI13227 x Lakin. Phytopathology https://doi.org/10.1094/PHYTO-09-16-0347-R