A new interspecific, Gossypium hirsutum × G. barbadense, RIL population: towards a unified consensus linkage map of tetraploid cotton

Abstract

We report the development of a new interspecific cotton recombinant inbred line (RIL) population of 140 lines deriving from an interspecific cross between Gossypium hirsutum (Gh) and G. barbadense (Gb), using the same two parents that have served for the construction of a BC(1) map and for the marker-assisted backcross selection program underway at CIRAD. Two marker systems, microsatellites and AFLPs, were used. An important feature of the RIL population was its marked segregation distortion with a genome-wide bias to Gh alleles (parental genome ratio is 71/29). The RIL map displays an excellent colinearity with the BC(1) map, although it is severely contracted in terms of map size. Existence of 255 loci in common (between 6 and 14 per chromosome) allowed the integration of the two data sets. A consensus BC(1)-RIL map based upon 215 individuals (75 BC1 + 140 RIL) was built. It consisted of 1,745 loci, spanned 3,637 cM, intermediate between the sizes of the two component maps, and constituted a solid framework to cross align cotton maps using common markers. The new RIL population will be further exploited for fiber property QTL mapping and eQTL mapping.

Construction of a linkage map and QTL mapping for fiber quality traits in upland cotton (Gossypium hirsutum L.)

“…Here we found many common characteristics of QTLs related to fiber quality traits as described in the previous reports involving interspecific maps [3,10,23,[33][34][35][36][37][38] and intraspecific maps [12,15,26,30,[39][40][41][42][43][44][45][46], although few common markers were used in the present research and the previous studies, and the maps covered different region parts of cotton genome, making it difficult to compare the common QTLs, some QTLs were detected and mapped on the same chromosomes and affect common traits. These include seven QTLs for fiber length located in the same chromosomal regions as reported earlier [10,26,34,41,42], two QTLs for fiber uniformity ratio located in the same chromosomal regions [43,46], two QTLs for fiber micronaire [10,43,44], three QTLs for fiber elongation [30,36,42,43,46,47], and 4 QTLs for fiber strength [26,34,36,43,44,46,47].…”

Development of a core set of SSR markers for the characterization of Gossypium germplasm

“…To make significant and timely advances in genetic improvement of cotton, portable DNA markers based on polymerase chain reaction (PCR) are needed for the tetraploid genome of cultivated cottons. Over the last decade, thousands of PCR-based DNA markers including simple sequence repeat (SSR) markers were identified and many were mapped in the cotton genome (Blenda et al 2006;Guo et al 2007;Lacape et al 2009;Yu et al 2011;Yu et al 2012). These cotton SSR markers were developed either from random enriched small genomic clones, large insert bacterial artificial chromosome (BAC) clones (or physical contigs) or expressed sequence tags (ESTs) of Gossypium species.…”

A Review of QTL Mapping in Cotton: Molecular Markers, Mapping Populations and Statistical Methods

“…Several methods have been pursued to develop SSR markers in cottons, including analysis of SSR-enriched small insert genomic DNA libraries (Richard and Beckman et al, 1995;Udall et al, 2006;Ince et al, 2010 andKalia et al,2011), SSR mining from ESTs (Shaheen et al, 2009) and large-insert BAC derivation by end sequence analysis (Reddy et al, 2002). Cotton researchers have explored simple sequence repeats (SSRs) for studies of the phylogenetic and diversity analysis (Lacape et al, 2007) genetic mapping Lacape et al, 2009;Park et al, 2005;Xiao et al, 2009;Yu et al, 2011;Yu et al, 2013 andGore et al, 2014), association mapping (Kantartzi et al, 2008).…”