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United States Department of Agriculture

Agricultural Research Service

Related Topics

Research Project: Bridging Genomics and Plant Breeding with a Cotton Nested Association Mapping Population

Location: Plant Physiology and Genetics Research

2013 Annual Report

1a. Objectives (from AD-416):
Phenotypic variation of the majority of agronomically important crop traits is under polygenic control and understanding the genetic and molecular basis of this variation within and between populations will be essential for connecting genes and alleles to phenotypes. The Nested Association Mapping (NAM) strategy facilitates the linking of genotypes to phenotypes by combining the advantages of both linkage analysis and association mapping to dissect the genetic architecture of complex traits in a single, unified mapping population. The Maize Diversity group ( pioneered this strategy by constructing the first NAM population— a reference design of 25 families of 200 recombinant inbred lines (RILs) per family. The maize NAM population has provided unprecedented insight into the underlying genetics of developmental, morphological, and disease resistance traits and has become the nexus of community mapping resources in maize. The primary objectives of this study are to (i) select diverse founders that maximize genetic diversity, and (ii) construct a cotton NAM population of 3,000 F5 recombinant inbred lines.

1b. Approach (from AD-416):
The panel of 480 cotton inbred lines was assembled to capture the genes and alleles that form the genetic backbone of modern temperate elite lines. Before selecting diverse founders for constructing a NAM population, we need to molecularly characterize the genetic structure and diversity among the 480 cotton inbred lines. To that end, we propose to continue genotyping the panel with a total of 150 sub-genome specific SSR markers at genome-wide coverage. Not only will this enable definitive selection of NAM founder lines, but also it will provide tremendous insight into the patterns of genetic diversity among different breeding subpopulations. The crossing of 15 diverse founders to the two reference parents, Acala Maxxa and TM-1, will be completed this winter in the greenhouse, followed by selfing of F1 plants in summer 2012. This will allow for the availability of F2 seed for advancement to the F5 generation by single-seed descent in Tecoman from fall 2012 to fall 2013. The large-scale seed increase of all F5 lines would begin in spring 2014. Presently, we are targeting the development of 100 RILs for each of 30 families (15 diverse founders X 2 reference parents). The selection of Acala Maxxa as a reference parent enables the integration of this project with that of the exotic cotton NAM population (PI Andrew Paterson). As a genetic complement to the cotton NAM population, the subset of 384 diverse lines will be seed increased in the 2011/2012 Tecoman winter nursery. The other 96 lines of the panel need an additional round of selfing to improve uniformity, followed by seed increasing in Tecoman before inclusion for phenotyping. We will begin phenotyping a single replication (augmented alpha-lattice design) of the 384 lines at NC, SC, and AZ locations in 2012, followed by phenotyping of the 480 lines at the same three locations in 2013. This population will be invaluable as a community resource for genome-wide association studies and training statistical models in genomic selection. Therefore, as with the cotton NAM population, seed of these 480 lines will be deposited in the USDA-ARS National Cotton Collection in College Station, Texas. This will increase the availability of these mapping resources to the global cotton community.

3. Progress Report:
This agreement is in support of objective 2 of the parent project, "Develop improved germplasm resources for abiotic stress resistance and fiber quality in Gossypiumbarbadense and G. hirsutum utilizing and integrating classical and biotechnology-based methodologies", and subobjective 2.a, "Develop improved germplasm resources for abiotic stress resistance and fiber quality in G. hirsutum utilizing and integrating classical and biotechnology-based methodologies". The study had the main goal to construct an upland cotton association mapping population. Based on preliminary assessment, parents have now been selected to develop a cotton nested association mapping (NAM) population, and hybridized. In collaboration with North Carolina State, an ARS scientist at Maricopa, Arizona, the collaborative group has genotyped 384 upland cotton inbred lines with 120 fluorescent-labeled microsatellite markers on an ABI 3730 capillary sequencer. Preliminary results show that these 384 lines capture an average of 4.8 alleles per locus, and of these lines, 50 of them have now been chosen and maximizing genetic diversity and crossed as males to two reference parents. A second set of 96 cotton lines are now undergoing a second round of single plant selfing to reduce heterozygosity levels this summer in North Carolina. In collaboration with North Carolina State and University of Arkansas, ARS scientists at Florence, South Carolina, and Maricopa, Arizona, planted seed for 348 of the 384 lines that had quantities of seed for evaluation at four locations (Arizona, North Carolina, South Carolina, and Arkansas). We used an augmented, incomplete block design at each location because of the large scale of this experiment. This experimental design required the use of several check varieties in each block to allow estimation of within-environment block effects and error variances. The population is being evaluated for yield and fiber quality traits, with fully analyzed data expected soon. This study will generate new genetic mapping resources and genetic markers associated with yield and fiber quality traits in cotton.

4. Accomplishments

Last Modified: 06/24/2017
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