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United States Department of Agriculture

Agricultural Research Service

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

Location: Plant Physiology and Genetics Research

2012 Annual Report


1a.Objectives (from AD-416):
The primary objectives of this study are to (i) select diverse founders that maximize genetic diversity, and (ii) construct a cotton population of several thousand F5 recombinant inbred lines.


1b.Approach (from AD-416):
A 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 nested association mapping (NAM) population of several thousand F5 recombinant inbred lines, we need to molecularly characterize the genetic structure and diversity among the 480 cotton inbred lines. To that end, we propose to genotype this panel with more than 100 sub-genome specific SSR markers at genome-wide coverage. Not only will this enable definitive selection of founder lines, but also it will provide tremendous insight into the patterns of genetic diversity among different breeding subpopulations. The crossing of diverse founders to a common reference parent 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 100-200 RILs for each family.

As a genetic complement to the cotton NAM population, a 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 Trust Agreement is in support of objective 2 of the parent project- Develop improved germplasm resources for abiotic stress resistance and fiber quality in Gossypium barbadense and G. hirsutum utilizing and integrating classical and biotechnology-based methodologies, 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 present study was conducted to construct an upland cotton association mapping population and select parents to develop a cotton nested association mapping (NAM) population. In collaboration with North Carolina State, an ARS scientist at Maricopa, AZ, 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. Of the 384 lines, 50 of them that maximize genetic diversity will be crossed as males to two reference parents. If crossings are not completed this summer in North Carolina, they will be performed in greenhouses this winter. A second set of 96 cotton lines will undergo a second round of single plant selfing to reduce heterozygosity levels this summer in North Carolina. In collaboration with North Carolina State University and University of Arkansas, ARS scientists at Florence, SC, and Maricopa, AZ, planted seed for 348 of the 384 lines that had quantities of seed for evaluation at four locations (AZ, NC, SC, and AR). Because of the scale of this experiment, we used an augmented, incomplete block design at each location. This experimental design requires the use of several check varieties in each block to allow estimation of within-environment block effects and error variances. The population will be evaluated for yield and fiber quality traits. This research will result in the construction of genetic mapping resources and genetic markers associated with yield and fiber quality traits. Progress performance has been monitored through discussion of project plans, reviewing program goals and accomplishments at ARS facilities, teleconference, e-mail, and quarterly reports.


Last Modified: 9/20/2014
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