2012 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 www.cottonmarker.org). 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 agreement is in support of objective 1C and objective 3 of the approved in-house project, the goal being to map selected cotton chromosomes and identify genes responsible for resistance to root knot nematode and Fusarium wilt, both of which cause yield losses in cotton. Previously identified regions of cotton chromosomes 11 and 21 from two sources, root-knot nematode susceptible cv. Acala Maxxa and root-knot nematode resistant N901 (cv. Acala NemX), were examined for resistance elements using more than 500 simple sequence repeats and other sequence data. Preliminary analyses and comparisons of sequences against published databases revealed the presence of DNA regions similar to known resistance genes. 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.