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United States Department of Agriculture

Agricultural Research Service

Research Project: Germplasm Enhancement and Genetic Improvement of Cotton
2012 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:
Useful genetic diversity is needed in cotton breeding programs. To capitalize on genetic diversity among exotic photoperiodic accessions, day neutral (DN) selections were made in 70 F2 populations of exotic race stocks by a DN donor cultivar. Seventy-five photoperiodic exotic race lines were crossed or backcrossed to a DN donor parent to add needed diversity to cotton germplasm. New sources of resistance to the tobacco budworm are needed in cotton. Forty-two day-neutral derived accessions were evaluated in field plots artificially infested with tobacco budworm. None of these lines exhibited resistance. Thirty diverse DN accessions from our research program were crossed to four diverse cultivars and a random mating population was developed. To assess genetic diversity of primitive cotton accession, 875 F4 DN lines were grown. Deoxyribonucleic acid (DNA) was extracted and molecular markers used to assess diversity. New chromosome substitution lines for six different chromosomes of Gossypium (G) tomentosum, eight different chromosomes of G. mustellinum, and four different chromosomes of G. barbadense were developed. Association of cryptic alleles in chromosomes 9 and 10 from G. barbadense were found for agronomic traits. Completed the genotyping and quantitative trait analysis of G. barbadense substitution lines for short arm of chromosomes 5 and 17 Recombinant Inbred Lines (RIL). Completed field evaluation on agronomic and fiber quality traits and genotyping of 43 improved cultivars with 582 Simple Sequence Repeat (SSR) marker loci and discovered several markers including chloroplast specific markers are associated with important fiber trait. Ribonucleic acid (RNA) was extracted from root-knot nematode (RKN)-infected resistant and susceptible plants along with uninoculated controls at four time-points after infection. Detection of known defense gene induction, i.e. meloidogyne induced cotton gene (MIC3), was greatest in resistant plants at the first time-point; therefore, RNAs corresponding to this time-point were selected for high-throughput RNA sequence analysis. Approximately 20 Mb of RNA sequence was obtained for each sample and assembled into contigs that represent individual genes. The relative abundance of each gene in each RNA sample was determined to identify genes differentially expressed between resistant and susceptible plants following RKN infection. The susceptibility of R2 MIC3 over-expressing transgenic lines to RKN, reniform nematode (RN), and Heliothis zea was determined. The transgenic lines showed increased resistance to RKN but not to RN or H. zea. Thirty-one candidate RN parasitism genes were analyzed for their expression during nematode development, and 11 were highly expressed during the parasitic life-stage which may indicate involvement in establishing the nematode feeding site. In situ hybridizations are in progress to determine whether these eleven genes are expressed within the RN gland cells. In addition, DNA vectors designed for nematode gene silencing experiments were acquired and are being prepared for use in RNA-interference studies with these candidate parasitism genes.


4.Accomplishments
1. Reniform nematode (RN) resistance from exotic accession T2468 transferred to Upland cotton. The RN has become a serious pest of cotton in the Mid-south during the last decade. Sources of resistance within Upland, Gossypium hirsutum, are needed. The Genetics and Precision Agriculture Research Unit at Mississippi State, MS, developed three resistant germplasm lines from photoperiodic accession T2468 and released seed of these lines to breeders. These lines suppress nematode reproduction to approximately 50% of that of a susceptible check. The moderately resistant lines exhibit considerable differences for agronomic and fiber traits and should be valuable to commercial cotton breeding programs.

2. Reniform nematode (RN) resistance from GB713 transferred to Upland cotton. To combat the expanding RN pest problem in cotton production higher levels of plant resistance are need. The Genetics and Precision Agriculture Research Unit at Mississippi State, MS, transferred a high level of resistance from Gossypium barbadense accession GB713 into Upland cotton by crossing and backcrossing to Sure-Grow 747. Marker assisted selection (MAS), using markers we had previously discovered for three genes, was used to identify resistant plants following each cross and backcross. Following the second backcross resistance of selected plants was verified in greenhouse tests where nematode reproduction was suppressed by approximately 90% of a susceptible check. A germplasm release of these resistant lines was made, and seed were distributed to breeders. A germplasm registration has been submitted to the Journal of Plant Registrations. This highly resistant RN germplasm and corresponding molecular markers will be valuable for breeders and ultimately for cotton growers.

3. Improved agronomic and fiber traits transferred from Gossypium (G.) barbadense to Upland cotton. The Genetics and Precision Agriculture Research Unit at Mississippi State, MS, developed a random mated cotton population involving 18 chromosome substitution lines from G. barbadense and 3 diverse Upland varieties. Following 5 cycles of random mating a germplasm release was made and germplasm registration was submitted to the Journal of Plant Registrations. Seed will be sent to geneticists and breeders in 2012. This is a unique population which has a considerable number of alleles from G. barbadense introgressed into Upland cotton and offers useful agronomic and fiber alleles for use in cotton variety development.


Review Publications
Jenkins, J.N., McCarty Jr., J.C., Wubben, M.J., Hayes, R.W., Gutierrez, O.A., Callahan, F.E., Deng, D.D. 2012. SSR markers for marker assisted selection of root-knot nematode (Meloidogyne incognita) resistant plants in cotton (Gossypium hirsutum L.). Euphytica. 183:49-54.

McCarty, Jr., J.C., Jenkins, J.N., Wubben, M., Hayes, R.W., Lafoe, M. 2012. Registration of three germplasm lines of cotton derived from Gossypium hirsutum L. accession T2468 with moderate resistance to the reniform nematode. Journal of Plant Registrations. 6:85-87.

Saha, S., Stelly, D.M., Raska, D.A., Wu, J., Jenkins, J.N., McCarty, Jr., J.C., Makamov, A., Gotmare, V., Abudurakhmonov, I., Campbell, B.T. 2012. Chromosome substitution lines: Concept, development and utilization in the genetic improvement of upland cotton. In: Abdurakhmoov, I.Y., editor. Plant Breeding. InTech. p. 107-128.

Wu, J., Jenkins, J.N., McCarty Jr., J.C., Lou, X. 2011. Comparisons of four approximation algorithms for large-scale linkage map construction. Theoretical and Applied Genetics. 123:649-655.

Yu, J., Kohel, R.J., Fang, D.D., Cho, J., Van Deynze, A., Ulloa, M., Hoffman, S.M., Pepper, A.E., Stelly, D.M., Jenkins, J.N., Saha, S., Kumpatla, S.P., Shah, M.R., Hugie, W.V., Percy, R.G. 2012. A high-density simple sequence repeat and single nucleotide polymorphism genetic map of the tetraploid cotton genome. Genes, Genomes, Genetics. 2:43-58.

Gao, W., Saha, S., Ma, D., Guo, Y., Jenkins, J.N., Stelly, D.M. 2012. A cotton-fiber-associated cyclin-dependent kinase A gene: Characterization and chromosomal location. International Journal of Plant Genomics. 2012:613812.

Buyyarapu, R., Kantety, R.V., Yu, J., Saha, S., Sharma, G.C. 2011. Development of new candidate gene and EST-based molecular markers for Gossypium species. International Journal of Plant Genomics. 2011:Article 894598.

Wubben, M.J, Ganji, S., Callahan, F.E. 2010. Identification and molecular characterization of a glycosyl hydrolase family 5 B-1,4-endoglucanase (Rr-eng-1) from the reniform nematode, Rotylenchulus reniformis. Journal of Nematology. 42:342-351.

Abdurakhmonov, I.K., Buriev, Z.T., Shermatov, S.E., Abdullaev, A.A., Urmonov, K., Kushanov, F., Egamberdiev, S.S., Shapulatov, U., Abdukarimov, A., Saha, S., Jenkins, J.N., Kohel, R.J., Yu, J., Pepper, A.E., Kumpatala, S., Ulloa, M. 2012. Genetic diversity in Gossypium genus. In: Caliskan, M., editor. Genetic Diversity in Plants. InTech. p. 313-338.

Last Modified: 10/25/2014
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