A high density SLAF-seq SNP genetic map and QTL for seed size, oil and protein content in upland cotton

Abstract

Background Cotton is a leading natural fiber crop. Beyond its fiber, cottonseed is a valuable source of plant protein and oil. Due to the much higher value of cotton fiber, there is less consideration of cottonseed quality despite its potential value. Though some QTL controlling cottonseed quality have been identified, few of them that warrant further study are known. Identifying stable QTL controlling seed size, oil and protein content is necessary for improvement of cottonseed quality. Results In this study, a recombinant inbred line (RIL) population was developed from a cross between upland cotton cultivars/lines Yumian 1 and M11. Specific locus amplified fragment sequencing (SLAF-seq) technology was used to construct a genetic map that covered 3353.15 cM with an average distance between consecutive markers of 0.48 cM. The seed index, together with kernel size, oil and protein content were further used to identify QTL. In total, 58 QTL associated with six traits were detected, including 13 stable QTL detected in all three environments and 11 in two environments. Conclusion A high resolution genetic map including 7033 SNP loci was constructed through specific locus amplified fragment sequencing technology. A total of 13 stable QTL associated with six cottonseed quality traits were detected. These stable QTL have the potential for fine mapping, identifying candidate genes, elaborating molecular mechanisms of cottonseed development, and application in cotton breeding programs. Electronic supplementary material The online version of this article (10.1186/s12864-019-5819-6) contains supplementary material, which is available to authorized users.

Identification and analysis of oil candidate genes revealed the molecular basis of oil accumulation in Gossypium hirsutum L. for cottonseed biofuels development

“…With the development of SNP arrays, sequencing and genotyping technologies, an increasing number of QTL mapping about cottonseed oil studies recently have been carried out [36][37][38][39][40]. This study developed an intra-speci c RIL population in upland cotton for QTL mapping, which consisting of 196 lines with the parents 0-153 and sGK9708.…”

Construction of a High-Density Genetic Map via Genome Resequencing and QTL Detection for Key Fiber Traits in Asiatic Cotton

“…In recent years, SNP (single nucleotide polymorphism) molecular marker has become popular in high-density genetic map construction, QTL mapping and marker assisted selection (MAS) due to its abundance in plant genome and advancement in next generation sequencing (NGS) [13][14][15]. And many NGS-related approaches have been developed to identify SNPs in cotton, such as whole genome resequencing [16,17], restriction site-associated DNA sequencing (RAD-seq) [18,19], speci c locus ampli ed fragment sequencing (SLAF-seq) [20][21][22] and genotyping-by-sequencing (GBS) [23,24]. In addition, the release of genome sequences of cotton species including G. arboreum [16], G. raimondii [25], G. hirsutum [26] and G. barbadense [27] made it easy to construct genetic map and detect QTL via NGS technology.…”

Identification of QTL and QEI for Fiber-related Traits in Gossypium Hirsutum L. 

“…Single nucleotide polymorphism (SNP) markers with genome wide abundance characterized by high-throughput genotyping can meet the requirement for high density genetic map construction and QTL dissection. In recent years, a lot of QTL for yield, ber quality and other agronomic traits have been identi ed with SNP marker genetic maps in cotton, including restriction-site associated DNA sequencing (RAD-seq) [11,12], genotyping-by-sequencing (GBS) [13,14], ampli ed fragment sequencing (SLAF-seq) [15][16][17][18], and SNP-array [19]. In addition to ber, cotton is also regarded as the most important source of vegetable protein and oil [20,21].…”

“…Our previous studies have shown that major QTL for lint percentage, crude protein content, crude oil content and ber quality traits are identi ed at morphological loci N 1 , Lc 1 , and Lg [26,27]. Our recent study has constructed a high density SLAF-seq SNP genetic map and identi ed QTL for seed size, oil and protein content with a RIL population developed from a cross between high ber quality cultivar Yumian 1 and high oil content line M11 [18]. This study identi ed QTL for ber-related traits and QTL by environment interactions (QEI) under four different environments.…”