A comprehensive meta QTL analysis for fiber quality, yield, yield related and morphological traits, drought tolerance, and disease resistance in tetraploid cotton

Abstract

BackgroundThe study of quantitative trait loci (QTL) in cotton (Gossypium spp.) is focused on traits of agricultural significance. Previous studies have identified a plethora of QTL attributed to fiber quality, disease and pest resistance, branch number, seed quality and yield and yield related traits, drought tolerance, and morphological traits. However, results among these studies differed due to the use of different genetic populations, markers and marker densities, and testing environments. Since two previous meta-QTL analyses were performed on fiber traits, a number of papers on QTL mapping of fiber quality, yield traits, morphological traits, and disease resistance have been published. To obtain a better insight into the genome-wide distribution of QTL and to identify consistent QTL for marker assisted breeding in cotton, an updated comparative QTL analysis is needed.ResultsIn this study, a total of 1,223 QTL from 42 different QTL studies in Gossypium were surveyed and mapped using Biomercator V3 based on the Gossypium consensus map from the Cotton Marker Database. A meta-analysis was first performed using manual inference and confirmed by Biomercator V3 to identify possible QTL clusters and hotspots. QTL clusters are composed of QTL of various traits which are concentrated in a specific region on a chromosome, whereas hotspots are composed of only one trait type. QTL were not evenly distributed along the cotton genome and were concentrated in specific regions on each chromosome. QTL hotspots for fiber quality traits were found in the same regions as the clusters, indicating that clusters may also form hotspots.ConclusionsPutative QTL clusters were identified via meta-analysis and will be useful for breeding programs and future studies involving Gossypium QTL. The presence of QTL clusters and hotspots indicates consensus regions across cultivated tetraploid Gossypium species, environments, and populations which contain large numbers of QTL, and in some cases multiple QTL associated with the same trait termed a hotspot. This study combines two previous meta-analysis studies and adds all other currently available QTL studies, making it the most comprehensive meta-analysis study in cotton to date.

Genetic Mapping in Cotton

“…A total of 151 staple length QTLs were reported over the entire genome except chromosomes C2 and C22 [91]. In total 12 marker-trait association for staple length were reported in earlier study [125].…”

“…A total of 25 QTLs conferring lint production were reported over the entire genome but none of the chromosome contained more than three QTLs [91]. Qin et al [125] reported 17 associated markers with lint percentage.…”

“…Said et al [91] identified 234 QTLs for micronaire value, which were spread over the entire genome of cotton. Most of these micronaire QTLs were on chromosome no.…”

“…The textile industry requires yarn of high average strength so that it can help to counter harsh spinning activities [163,164]. Said et al [91] reported 132 fiber bundle strength QTLs, which were spread over the entire genome with the exception of chromosome no. 17 which contained none.…”

“…However, association mapping achieved for crop improvement is not comparable to that in human genomics [89]. Over the decades, many QTLs have been identified using bi-parental populations for yield, yield components and other traits of interest [90,91]. However, only few were successfully used in plant improvement programs.…”