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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

2009 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 reombinant 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
Day neutral selections from T-2468 have significant levels of resistance to the reniform nematode. This resistance is valuable for cotton breeding. Day-neutral selections were made in 96 F2 populations of exotic race stocks. Fifty new photoperiodic exotic race lines were crossed to a day neutral donor parent. This germplasm will be used in cultivar development programs. Thirty diverse day-neutral accessions were crossed to four diverse cultivars to begin development of a random mating population. Quality trait loci (QTL) analysis of photoperiodic accessions suggested at least three chromosomes contain factors associated with flowering. Developed 232 recombinant inbred lines (RIL) from our random mating population RMUPC5S1 and evaluated for agronomic and fiber properties. Genes differentially expressed between root-knot nematode (RKN)-resistant and susceptible plants discovered using GeneFishing technology (Seegene, Inc.). Two partial cDNAs have been cloned from resistant M315 root-knot nematode resistant (RNR) RKN-infected root tissue that are absent in susceptible DPL90 RKN-infected roots. Time-course experiments of reniform infection are currently being conducted to identify the optimal stage to collect ribonucleic acid (RNA) for differential expression of genes. We are developing transgenic cotton plants that over-express MIC3. The RKN-susceptible obsolete cultivar, Coker 312, was transformed with a MIC3 over-expression construct at the ARS Plant Stress and Germplasm Development Research Unit in Lubbock, TX. T1 seed from transgenic plants from 7 independent transformation events will be shipped to our location at Mississippi State in Fall 2009 for molecular and nematode infection assessments. A cDNA library has been constructed using total RNA isolated from sedentary, parasitic female reniform nematodes. Clone sequencing and bioinformatic analyses are currently underway. Substituted Gossypium barbadense chromosomes of 3-79 harbor cryptic beneficial alleles with potential to improve agronomic and fiber traits. Determined agronomic and fiber traits of 4 new CS-B lines. Significant epistatic effects associated with the substituted chromosomes of 3-79. Completed field evaluation of fiber and agronomic traits of four new CS-B NTN lines. Developed six new chromosome substitution lines from G. tomentosum (CS-T01, CS-T04, CS-T07, CS-T18, CS-T8Lo, CS-T15Lo). Cloned and sequenced MIC-3 genes from selected diploid and tetraploid cotton species revealed structural differences at the molecular level and identified clustering of a cotton gene family associated with resistant response. MIC-3 gene family revealed MIC-3 members in Dt genome under strong positive selection whereas they are under strong purifying selection in At genome of the tetraploid cotton (AtDt). Such complementary buffering of MIC-3 genes in alternative genomes of tetraploid cotton indicates a fitness advantage useful to cotton for combating evolving pests and pathogens.


Review Publications
Guo, Y., McCarty Jr., J.C., Jenkins, J.N., Saha, S. 2008. QTLs for node of first fruiting branch in a cross of an upland cotton, Gossypium hirsutum L., cultivar with primitive accession Texas 701. Euphytica. 163:113-122.

Robinson, A.F., Bell, A.A., Augudelo, P., Avila, C.A., Stewart, J.M., Callahan, F.E., Hayes, R.W., Jenkins, J.N., McCarty, J.C., Wubben, M.J., Cook, C.G., Dighe, N.D., Menz, M.A., Smith, C.W., Stelly, D.M., Gutierrez, O.A., Wallace, T.P., Johnson, J.T., Kantety, R., Lawrence, G.W., Lawrence, K.S., Mangineni, L., Weaver, D.B., Meredith, W.A., Sacks, E., Scheffler, B., Stetina, S.R., Young, L.D., Nichols, R.L., Robbins, R.T., Sciumbato, G.L., Thaxton, P.M., Starr, J.L. 2008. Development of reniform nematode resistance in Upland cotton. In: Proceedings of the World Cotton Research Conference-4, September 10-14, 2007, Lubbock, Texas. 2008 CDROM.

Abdurakhmonov, I.Y., Abdullaev, A.A., Saha, S., Buriev, Z.T., Arslanov, D., Kuryazov, Mavlonov, G., Rizaeva, S.M., Reddy, U.K., Jenkins, J.N., Abdullaev, A., Abdukarimov, A. 2005. Simple sequence repeat marker associated with a natural leaf defoliation trait in tetraploid cotton. Journal of Heredity. 96:644-653.

Jenkins, J.N., McCarty Jr., J.C., Gutierrez, O.A., Hayes, R.W., Bowman, D.T., Watson, C.E., Jones, D.C. 2008. Registration of RMUP-C5, a random mated population of Upland cotton germplasm. Journal of Plant Registrations. 2:239-242.

Wu, J., Gutierrez, O. A., Jenkins, J.N., McCarty Jr., J.C., Zhu, J. 2009. Quantitative analysis and QTL mapping for agronomic and fiber traits in an RI population of Upland cotton. Euphytica. 165:231-245.

Saha, S., Jenkins, J.N., Wu, J., McCarty Jr., J.C., Stelly, D.M. 2008. Genetic analysis of agronomic and fiber traits using four interspecific chromosome substitution lines in cotton. Plant Breeding. 127:612-618.

Siebert, W.M., Babcock, J.M., Nolting, S., Santos, A.C., Adamczyk Jr, J.J., Neese, P.A., King, J.E., Jenkins, J.N., Lorenz, G.M., Fromme, D.D., Lassiter, R.B. 2008. Efficacy of Cry1F insecticidal protein in maize and cotton for control of fall armyworm (Lepidoptera: Noctuidae). Florida Entomologist. 91(4):555-565.

Guo, Y., McCarty Jr., J.C., Jenkins, J.N., An, C., Saha, S. 2009. Genetic detection of node of first fruiting branch in crosses of a cultivar with two exotic accessions of upland cotton. Euphytica. 166:317-329.

Gutierrez, O.A., Stelly, D.M., Saha, S., Jenkins, J.N., McCarty Jr., J.C., Raska, D.A., Scheffler, B.E. 2009. Integrative placement and orientation of non-redundant SSR loci in cotton linkage groups by deficiency analysis. Molecular Breeding. 23:693-707.

Jenkins, J.N., McCarty Jr., J.C., Wu, J., Gutierrez, O. 2009. Genetic variance components and genetic effects among eleven diverse upland cotton lines and their F2 hybrids. Euphytica. 167:397-408.

Wu, J., Jenkins, J.N., McCarty Jr., J.C., Thaxton, P. 2009. Seed trait evaluation of Gossypium barbadense L. chromosomes/arms in a G. hirsutum L. background. Euphytica. 167:371-380.

Wallace, T.P., Bowman, D., Campbell, B.T., Chee, P., Gutierrez, O.A., Kohel, R.J., McCarty, J., Myers, G., Percy, R., Robinson, F., Smith, W., Stelly, D.M., Stewart, J.M., Thaxton, P., Ulloa, M., Weaver, D.B. 2009. Status of the USA cotton germplasm collection and crop vulnerability. Genetic Resources and Crop Evolution 56:507-532.

Gutierrez, O.A., Wubben, M., Howard, M., Roberts, B., Hanlon, E., Wilkinson, J.R. 2009. Role of phytohormones ethylene and auxin in plant-nematode interactions: mini-review. Russian Journal of Plant Physiology. 56:1-5.

Abdurakhmonov, I.Y., Saha, S., Jenkins, J.N., Buriev, Z.T., Shermatov, S.E., Scheffler, B.E., Pepper, A.E., Yu, J., Kohel, R.J., Abdukarimov, A. 2009. Linkage disequilibrium based association mapping of fiber quality traits in G. hirsutum L. variety germplasm. Genetica. 136:401-417.

Myers, G.M., Jiang, B., Akash, M.W., Badigannavar, A., Saha, S. 2009. Chromosomal assignment of ALFP markers in upland cotton (Gossypium hirsutum L.). Euphytica. 165:391-399.

Abdurakhmonov, I.Y., Buriev, Z.T., Saha, S., Pepper, A.E., Musaev, J.A., Almatov, A., Shermatov, S.E., Kushanov, F.N., Mavlonov, G.T., Reddy, U.K., Yu, J., Jenkins, J.N., Kohel, R.J., Abdukarimov, A. 2007. Microsatellite markers associated with lint percentage trait in cotton, Gossypium hirsutum. Euphytica. 156:141-156.

Wu, J., Jenkins, J.N., McCarty Jr., J.C., Saha, S., Percy, R.G. 2008. Genetic association of lint yield with its components in cotton chromosome substitution lines. Euphytica. 164:199-207.

Last Modified: 7/30/2014
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