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United States Department of Agriculture

Agricultural Research Service

Research Project: Germplasm Enhancement and Genetic Improvement of Cotton

Location: Genetics and Sustainable Agriculture Research

2010 Annual Report

1a. Objectives (from AD-416)
Develop and evaluate cotton breeding populations with new combinations of alleles useful for cultivar improvement. Apply molecular marker technologies to identify and characterize genetic variation in cotton germplasm lines. Identify and characterize molecular determinants for nematode infection of cotton and apply knowledge to accelerating breeding programs. Apply or modify genetic analyses which accelerate the identification and incorporation of novel sources of superior agronomic traits for breeding cotton.

1b. Approach (from AD-416)
Alleles from mostly photoperiodic, exotic accessions will be incorporated into breeding populations. Chromosome substitution and recombinant inbred lines will be developed, breeding populations useful for nematode resistance will be generated, and the evaluation of germplasm lines for resistance to nematodes and improved fiber quality will be conducted. Use molecular marker technologies to identify and characterize genetic variation for host plant resistance to root-knot nematode and reniform nematode, and improved agronomic and fiber quality. Resistance responses to root-knot and reniform infection will be characterized. The functional relevance of the MIC3 gene to nematode resistance will be determined, and a functional genetics platform for the reniform nematode to identify potential target genes for RNA-inference will be developed. Use linkage disequilibrium and association mapping to identify novel sources of superior agronomic, pest resistance, and fiber traits.

3. Progress Report
The genetic base for cultivar development needs to be expanded. Day neutral selections were made in 100 F2 populations of exotic race stocks. Useful diversity in the day neutral lines can improve commercial cotton cultivars. Fifty new crosses with exotics were made which can ultimately feed into cultivar development. Thirty diverse day neutral accessions were crossed to four diverse cultivars, and a random mating population is being developed. Resistance genes are needed for the reniform nematode. Day neutral, resistant plant selections were made using marker assisted selection from the cross of SG747 by GB713, a photoperiodic accession with reniform nematode resistance. Cotton seeds provide a desirable and important nutrition profile. Seed protein, oil, hull fiber content, embryo percentage and seed index were evaluated for 13 chromosome substitution lines and their F3 hybrids. A seed trait analysis model was developed. Genetic effects were detected and results show these seed traits can be genetically improved. An atypical phenotype was observed in ligon lintless-2, which typically has fuzzy seed with short lint fibers. Plants that expressed two phenotypes on the same plant (the typical ligon lintless phenotype and a normal phenotype of fuzzy seed with normal length lint fibers) were found, and we proposed these may be due to incomplete penetrance or lack of consistent expression on the mutant gene. Currently we are analyzing results of fiber and agronomic traits of four new chromosome substitution lines and a partial diallele cross among seven substitution lines. We have developed about 50 Recombinant Inbred Lines (RIL) for chromosomes 22Lo,22sh and 25, developed six new chromosome substitution lines from Gossypium (G.) tomentosum in G. hirsutum (chromosomes 1,4,7,18,8Lo and 15Lo), and are currently evaluating their performance. Cotton genes initially thought to be expressed differentially between root knot nematode (RKN) infected susceptible and resistant plants were further analyzed and found to be false positives. No other genes were identified using the GeneFishing method (Seegene, Inc.). We are now considering using next-generation complementary deoxyribonucleic acid (cDNA) sequencing (Roche 454 or Solexa) to characterize RKN-susceptible and RKN-resistant transcriptomes. Transgene-positive plants within 13 T1 families were identified for a total of 43 T1 plants. T1 and negative control plants were selfed and bolls containing T2 seed were collected in June 2010. We are determining which T2 families are homozygous for the MIC3 over-expression construct and the effects of this transformation on resistance to RKN. A cotton cDNA, GhRING1, was cloned and sequenced and its corresponding genes associated with fiber development. We discovered the promoter region of GhRING1 gene is expressed specifically in the tissues of anther and stipules. Completed DNA extraction of 42 improved lines and their field evaluation for improved agronomic and fiber traits for the first year in two locations for association mapping.

4. Accomplishments
1. Root Knot Nematode (RKN) is a Serious Pest of Cotton. RKN causes considerable loss in production each year (316,980 bales estimated loss in 2009). ARS Genetics and Precision Agriculture Research Unit scientists at Mississippi State, MS, in cooperation with Mississippi State University scientists discovered simple sequence repeat (SSR) markers linked to two quantitative trait loci on two different chromosomes in cotton. This discovery provides seed breeding companies with the molecular tools to easily utilize the previously released ARS resistance genes for this pest in the development of resistant cultivars which should solve a major production problem.

2. Reniform Nematode is a Serious Pest of Cotton. (203,720 bales estimated loss in 2009). ARS Genetics and Precision Agriculture Research Unit scientists at Mississippi State, MS, in cooperation with ARS scientist at College Station, TX, and Mississippi State University scientists discovered SSR marker genes for resistance genes in GB 713 which will be very valuable for marker assisted selection in commercial breeding programs. This source of resistance and associated markers genes can greatly speed up the development of reniform nematode resistant cultivars for use by growers.

3. Reniform nematode is a Serious Pest of Cotton. 203,720 bales estimated loss in 2009 in the southern United States. The mechanism(s) by which reniform nematode is able to parasitize cotton are unknown, which complicates the development of effective control measures. ARS Genetics and Precision Agriculture Research Unit scientists at Mississippi State, MS, have identified the sequences of more than 600 genes that are expressed by parasitic female reniform nematodes. The further study of these genes and their role in the reniform nematode life-cycle could lead to the development of novel control strategies for cotton producers.

4. Additional Sources of Genetic Diversity are Needed for Cotton Fiber Quality Improvement. ARS Genetics and Precision Agriculture Research Unit scientists at Mississippi State, MS, in cooperation with scientists at Texas A&M University used a partial diallel cross among six selected chromosome substitution lines and the inbred Texas Marker-1 (TM-1), and characterized fiber quality traits in four environments. Some of the substituted chromosomes from G. barbadense carried alleles with the potential to improve fiber quality in G. hirsutum. Chromosome substitution line research opens new paradigms in cotton breeding and genetics studies by providing a breeding methodology that greatly reduces the problems common to interspecific introgression at the whole genome level.

Review Publications
Saha, S., Wu, J., Jenkins, J.N., McCarty Jr., J.C., Hayes, R.W., Stelly, D. 2010. Genetic Dissection of Chromosome Substitution Lines of Cotton to Discover Novel Gossypium barbadense L. Alleles for Improvement of Agronomic Traits. Journal of Theoretical and Applied Genetics. 120:1193-1205.

An, C., Jenkins, J.N., McCarty Jr., J.C., Saha, S. 2010. Atypical Ligon Lintless-2 Phenotype in Cotton. Journal of Cotton Science. 14:13-16.

Wu, J., McCarty Jr., J.C., Saha, S., Jenkins, J.N., Hayes, R.W. 2009. Genetic Changes in Plant Growth and their Associations with Chromosomes from Gossypium hirsutum L. in G. hirsutum L. Genetica. 137:56-66.

Wubben, M., Callahan, F.E., Triplett, B.A., Jenkins, J.N. 2009. Phenotypic and Molecular Evaluation of Cotton Hairy Roots as a Model System for Studying Nematode Resistance. Plant Cell Reports. 28:1399-1409.

Buriev, Z.T., Saha, S., Abdurakhmonov, I.Y., Jenkins, J.N., Abdukarimov, A., Scheffler, B.E., Stelly, D.M. 2010. Clustering, haplotype diversity and locations of MIC-3: a unique root-specific defense-related gene family in upland cotton (Gossypium hirsutum L.). Theoretical and Applied Genetics. 120:587-606.

Wu, J., McCarty Jr., J.C., Jenkins, J.N. 2010. Cotton Chromosome Substitution Lines Crossed with Cultivars: Genetic Model Evaluation and Seed Trait Analyses. Theoretical and Applied Genetics. 120:1473-1483.

An, C., Jenkins, J.N., Wu, J., Guo, Y., McCarty Jr., J.C. 2010. Use of Fiber and Fuzz Mutants to Detect QTL for Yield Components, Seed, and Fiber Traits of Upland Cotton. Euphytica. 172:21-34.

Wubben, M., Callahan, F.E., Scheffler, B.E. 2010. Transcript Analysis of Parasitic Females of the Sedentary Semi-Endoparasitic Nematode Rotylenchulus reniformis. Molecular and Biochemical Parasitology. 172:31-40.

Last Modified: 08/20/2017
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