Genetic mapping of new cotton fiber loci using EST-derived microsatellites in an interspecific recombinant inbred line cotton population

Abstract

There is an immediate need for a high-density genetic map of cotton anchored with fiber genes to facilitate marker-assisted selection (MAS) for improved fiber traits. With this goal in mind, genetic mapping with a new set of microsatellite markers [comprising both simple (SSR) and complex (CSR) sequence repeat markers] was performed on 183 recombinant inbred lines (RILs) developed from the progeny of the interspecific cross Gossypium hirsutum L. cv. TM1 x Gossypium barbadense L. Pima 3-79. Microsatellite markers were developed using 1557 ESTs-containing SSRs (> or = 10 bp) and 5794 EST-containing CSRs (> or = 12 bp) obtained from approximately 14,000 consensus sequences derived from fiber ESTs generated from the cultivated diploid species Gossypium arboreum L. cv AKA8401. From a total of 1232 EST-derived SSR (MUSS) and CSR (MUCS) primer-pairs, 1019 (83%) successfully amplified PCR products from a survey panel of six Gossypium species; 202 (19.8%) were polymorphic between the G. hirsutum L. and G. barbadense L. parents of the interspecific mapping population. Among these polymorphic markers, only 86 (42.6%) showed significant sequence homology to annotated genes with known function. The chromosomal locations of 36 microsatellites were associated with 14 chromosomes and/or 13 chromosome arms of the cotton genome by hypoaneuploid deficiency analysis, enabling us to assign genetic linkage groups (LG) to specific chromosomes. The resulting genetic map consists of 193 loci, including 121 new fiber loci not previously mapped. These fiber loci were mapped to 19 chromosomes and 11 LG spanning 1277 cM, providing approximately 27% genome coverage. Preliminary quantitative trait loci analysis suggested that chromosomes 2, 3, 15, and 18 may harbor genes for traits related to fiber quality. These new PCR-based microsatellite markers derived from cotton fiber ESTs will facilitate the development of a high-resolution integrated genetic map of cotton for structural and functional study of fiber genes and MAS of genes that enhance fiber quality.

Natural Diversity in Flowering Responses of Arabidopsis thaliana Caused by Variation in a Tandem Gene Array

“…Segregation distortion in A. thaliana: In addition to the association of the early flowering-time phenotype to MAF2 insertion alleles, we observed segregation distortion favoring the MAF2 insertion alleles in BC 5 F 2 segregating lines. Segregation distortion has been widely reported in A. thaliana (Loudet et al 2002;Bikard et al 2009) and other plant species (Lu et al 2002;Park et al 2005;Koide et al 2008). In A. thaliana, chimeric genes, as well as duplicated genes that undergo divergent evolution, have been shown to lead to genetic incompatibilities (Bomblies et al 2007;Alcazar et al 2009;Bikard et al 2009).…”

A Microsatellite-Based, Gene-Rich Linkage Map Reveals Genome Structure, Function and Evolution in Gossypium

“…A-genome diploid cottons produce spinnable fibers and have been cultivated, while D-genome species produce very short and appressed fibers. Nevertheless, many quantitative trait loci (QTL) for fiber-related traits have been identified in the D-subgenome of tetraploid cotton ( Jiang et al 1998;Kohel et al 2001;Park et al 2005;Paterson et al 2003;Shen et al 2005;Ulloa et al 2005), suggesting that the D-genome contains important genes or regulators of fiber morphogenesis and fiber properties.…”

“…edu/projects/cotton) for cotton microsatellite database (CMD) involving all of the available cotton SSR information has been constructed (Blenda et al 2006). These SSR markers have been widely used in cotton genetic mapping (Reddy et al 2001;Zhang et al 2002;Han et al 2004;Nguyen et al 2004;Abdurakhmonov et al 2005;Song et al 2005;Park et al 2005;Frelichouski et al 2006;Han et al 2006). Recently, more cotton ESTs, mostly from different fiber developmental stages, were publicly released in GenBank (http://www.ncbi.nlm.…”

Genetic Mapping in Cotton

“…Moreover, RILs are populations which produce finely saturated genetic maps as recombination frequency is high. RILs have been used in cotton for identifying traits related to agronomic and fiber [5,53,74]. Doubled-haploids are the best populations for improving any trait as these are the ones having 100% purity.…”