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United States Department of Agriculture

Agricultural Research Service


Location: Plant Stress and Germplasm Development Research

2013 Annual Report

1a. Objectives (from AD-416):
The objective of this research is to map and saturate cotton chromosomes 11 and 21 with existing and new EST and BAC-end derived SSR, STS, and SNP markers to discover and validate marker-associations with genetic control of nematode and wilt resistance (R) genes on diverse cotton populations with different genetic backgrounds.

1b. Approach (from AD-416):
To map and saturate cotton chromosome 11 (formerly LG A03) and its homoeologous chromosome 21 (formerly LG D02), we will mine the existing molecular marker resources (in-house and Large numbers of microsatellite or SSR markers located in different cotton chromosomes are available for mapping. These molecular markers such as BAC-end sequence based SSR markers, and EST-based SNPs will be evaluated on different genetic backgrounds. Existing and new molecular-marker data from screened cotton populations segregating for pathogen resistant phenotype will be analyzed by statistical and genetic packages. Both qualitative and quantitative (QTL)-based mapping will be conducted to reveal markers associated with nematode and wilt resistance genes and their genetic positions in the R-gene cluster region. Pools and superpools of the BAC libraries will be screened with marker-primers and probes developed from R gene linked marker sequences (e.g. CIR316, BNL1231, and MUCS088) and from G. hirsutum cv., Maxxa BAC-end SSR sequences. Additional new markers will be generated by sequencing BAC clones which will be aligned in gene cluster regions. Several BAC clones will be sequenced, and their sequences will be analyzed for possible targets for R genes. Resistance genes/markers will be evaluated and validated for marker–R gene associations by screening the markers on additional populations from cotton crosses for which the progenies have been pathogen-resistance phenotyped. Documents NFCA with UC Riverside. Formerly 5303-21220-003-14N (11/10)

3. Progress Report:
The goal of this project is to identify marker-genes responsible for resistance to root knot nematode and Fusarium wilt, both of which cause yield losses in cotton. Marker-genes are being mapped to selected cotton chromosomes. Specifically, we have interest in chromosomes 11 and 21. These two chromosomes were found to harbor resistance (R) or pathogen-induced R genes. DNA sequence of previously mapped SSR markers revealed response elements to plant internal and external stimulus, stress, signaling process and cell death through Gene Ontology (GO), which performed the analysis of sequence-similarity to known genes. In addition, new DNA sequences of 22 BAC clones (each clone around 100,000 base pairs) revealed putative unigenes. GO functional profiling of these unigenes uncovered cellular growth and development processes; transport, translation, and metabolic functions; and stress response elements. Moreover, BAC sequences revealed the presence of genes that encode proteins containing a nucleotide-binding site (NBS) and C-terminal leucine-rich repeats (LRRs), which represent the major class of disease R genes. For the first time in cotton, a putative NBS-LRR gene is being reported within clusters and in the vicinity of discovered root-knot nematode and Fusarium wilt resistance marker-genes on chromosome 11 and 21. Genome sequencing and physical alignment of genomic regions into chromosomal maps are steps that will improve the accuracy of detecting R genes and gene functions of important biological processes in crops. Sequence information obtained through these studies can be used to develop improved tools to discover additional resistance genes, and to speed efforts to incorporate resistance genes into germplasm and breeding lines. Activities during the project were documented through presentations to cotton producers, commodity groups, and professional societies, and through telephone contacts and site visits with collaborator.

4. Accomplishments

Last Modified: 06/25/2017
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