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United States Department of Agriculture

Agricultural Research Service

Research Project: Germplasm Enhancement and Genetic Improvement of Cotton

Location: Genetics and Precision Agriculture Research

2011 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
Genetics and Precision Agriculture Research Unit scientists at Mississippi State, MS, have capitalized on untapped genetic diversity. Day-neutral selections were made in 75 F2 populations of exotic race stocks crossed with a day-neutral donor cultivar. Seed are being increased and agronomic evaluations will be conducted. Useful diversity in the day-neutral lines can be used to improve commercial cotton cultivars. Fifty photoperiodic exotic race lines were crossed or backcrossed to a day-neutral donor parent. These new crosses will add needed diversity to cotton germplasm which will ultimately feed into cultivar development programs. To enhance germplasm with resistance to reniform nematode, GB713, a photoperiodic accession with resistance, was crossed to SG747. Day-neutral plants were selected and resistance identified by marker assisted selection (MAS). Selected plants were backcrossed to SG747; MAS will be used to identify BC2F2 plants that are resistant. Enhanced reniform nematode resistance germplasm will be valuable for breeders and ultimately aid cotton growers in controlling this nematode, a serious cotton pest. New sources of resistance are needed for the tobacco budworm. Forty day-neutral derived primitive accession lines were evaluated in field plots artificially infested with insects. None of the lines evaluated exhibited resistance. Fiber strength is important in high speed spinning industry. High strength exotic derived lines by cultivar F2 populations were evaluated in field plots. Several populations were identified that possessed high strength and good yield potential. We identified (16) non-segregating transgenic 2 (T2) generation families that contain the meloidogyne induced cotton gene (MIC3) over-expression construct. The level of MIC3 expression in the homozygous T2 families was determined at the messenger ribonucleic acid (mRNA) and protein levels. Susceptibility assays of the transgenic lines to root-knot nematode (RKN), reniform nematode, and Heliothis zea have been initiated. Root tissue samples were collected from RKN-susceptible and RKN-resistant cotton plants at four time-points after RKN infection. Root tissues were also collected from uninfected control plants. Ribonucleic acid (RNA), representing the genes expressed within the tissue, is currently being extracted from each one of the samples. We plan to subject the RNAs to next-generation sequencing to identify the genes that are differentially expressed between susceptible and resistant cotton plants during RKN infection. We used a partial diallel cross among the selected six quasi-isogenic chromosome substitution from barbadense (CS-B) lines and the inbred Texas marker 1 (TM-1), and characterized fiber quality traits across four environments. The results indicated that the substituted chromosomes of 3-79 carried cryptic beneficial alleles with potential to improve both agronomic and fiber quality traits. We detected important fiber quality and agronomic traits associated with chromosome substitution lines CS-B09 and CS-B10.

1. Markers for genetic resistance to reniform nematode obtained in cotton. Reniform nematode is a serious pest in all cotton production areas of the United States. Annual losses are estimated to be as much as 300 pounds lint per acre in highly infested fields. ARS Genetics and Precision Agriculture Research Unit scientists at Mississippi State, MS, in cooperation with an ARS scientist at College Station, TX, and a scientist at Mississippi State University discovered simple sequence repeat (SSR) markers associated with resistant Gossypium bardadense accession GB713. Two quantitative trait loci (QTL) were located to chromosome 21 and one QTL to chromosome 18 that confer resistance. These markers provide the technology that allows cotton seed breeding companies to rapidly use this excellent source of resistance to reniform nematode in the development of resistant cultivars. Development of resistant cultivars will solve a major pest problem for cotton growers.

2. Markers for genetic resistance to root-knot nematode discovered in cotton. Root-knot nematode is a serious pest in all cotton production areas of the United States. ARS Genetics and Precision Agricultural Research Unit scientists at Mississippi State, MS, in cooperation with a scientist at Mississippi State University, validated their previously discovered simple sequence repeat (SSR) markers for two genes for resistance on chromosomes 11 and 14 and developed and published a breeding strategy that shows the usefulness of these markers for commercial breeding of root-knot resistant cultivars. Major seed breeding companies have informed the scientists that these markers will be very useful in their current development of resistant cultivars. Commercial interest is especially high due to the industry decision to immediately stop manufacturing the insecticide/nematicide, TEMIK. Development of root-knot nematode resistant cultivars will solve a major pest problem for cotton growers.

3. Breeding germplasm developed which introgressed agronomic and fiber quality genes from exotic accession into Upland. Useful genetic diversity is a requirement of successful breeding programs. The primitive accessions of Gossypium hirsutum can provide needed diversity but these accessions are not directly useful by commercial cotton breeders because of their photoperiodic and exotic nature. Scientists in the Genetics and Precision Agriculture Research Unit at Mississippi State, MS, have selected 30 of these accessions and have converted them to day-neutrality. They then developed a random mating population of these 30 accessions when crossed to four diverse commercial cultivars and randomly mated for 4 generations. This random mated population has useful genetic diversity for improved fiber and agronomic traits and it also provides the germplasm in a form that is directly useable by commercial seed breeding companies for commercial breeding of improved cultivars.

4. A germplasm population of Gossypium barbadense chromosome substitution lines has been developed for cotton breeders. Scientists in the Genetics and Precision Agriculture Research Unit at Mississippi State, MS, developed a random mated population of cotton that combines genes from 18 Gossypium barbadense substitution lines with genes from Upland cultivars as a better way to introgress superior fiber quality genes into Upland cotton. This population will be very useful to cotton breeders as a source of improved fiber quality genes.

Review Publications
Wu, J., McCarty Jr, J.C., Jenkins, J.N., Meredith Jr, W.R. 2010. Breeding potential of introgressions into cotton: genetic effects and heterosis. Plant Breeding. 129:526-532.

Gutierrez, O.A., Jenkins, J.N., McCarty Jr., J.C., Wubben, M., Hayes, R.W., Callahan, F.E. 2010. SSR markers closely associated with genes for resistance to root-knot nematode on chromosomes 11 and 14 of upland cotton. Theoretical and Applied Genetics. 121:1323-1337.

Wu, J., Jenkins, J.N., McCarty Jr., J.C., Saha, S. 2010. Genetic effects of individual chromosomes in cotton cultivars detected by using chromosome substitution lines as genetic probes. Genetica. 138:1171-1179.

Gutierrez, O., Robinson, A.F., Jenkins, J.N., McCarty Jr., J.C., Wubben, M., Callahan, F.E., Nichols, R.L. 2011. Identification of QTL regions and SSR markers associated with resistance to reniform nematode in Gossypium barbadense L. accession GB713. Theoretical and Applied Genetics. 122:271-280.

Saha, S., Wu, J., Jenkins, J.N., McCarty, J.C., Hayes, R.W., Stelly, D.M. 2011. Delineation of interspecific epistasis on fiber quality traits in Gossypium hirsutum by ADAA analysis of intermated G. barbadense chromosome substitution lines. Theoretical and Applied Genetics. 122:1351-1361.

Campbell, B.T., Saha, S., Jenkins, J.N., Park, W., Percy, R.G., Frelichowski, J.E., Mayee, C., Gotmare, V., Dessauw, D., Giband, M., Du, X., Jia, Y., Constable, G., Dillon, S., Abdurakhmonov, I.Y., Abdukarimov, A., Rizaeva, S.M., Adullaev, A.A., Barroso, P.V., Padua, J.G., Hoffman, L.V., Podolnaya, L. 2010. Status of the global cotton germplasm resources. Crop Science. 50:1161-1179.

Ho, M., Saha, S., Jenkins, J.N., Ma, D. 2010. Characterization and promoter analysis of a cotton ring-type ubiquitin ligase (E3) gene. Molecular Biotechnology. 46:140-148.

McCarty Jr., J.C., Cash, L., Jenkins, J.N. 2011. Effects of within-row plant spacings on growth, boll retention, and yield of four cotton cultivars. Mississippi Agricultural and Forestry Experiment Station Bulletin 1191. 12 p.

Abdurakhmonov, I.Y., Kohel, R.J., Yu, J., Pepper, A.E., Abdullaev, A.A., Kushanov, F.N., Salakhutdinov, I.B., Buriev, Z.T., Saha, S., Scheffler, B.E., Jenkins, J.N., Abdukarimov, A. 2008. Molecular diversity and association mapping of fiber quality traits in exotic G. hirsutum L. germplasm. Genomics. 92:478-487.

Last Modified: 4/23/2014
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