A MAGIC population-based genome-wide association study reveals functional association of GhRBB1_A07 gene with superior fiber quality in cotton

Abstract

BackgroundCotton supplies a great majority of natural fiber for the global textile industry. The negative correlation between yield and fiber quality has hindered breeders’ ability to improve these traits simultaneously. A multi-parent advanced generation inter-cross (MAGIC) population developed through random-mating of multiple diverse parents has the ability to break this negative correlation. Genotyping-by-sequencing (GBS) is a method that can rapidly identify and genotype a large number of single nucleotide polymorphisms (SNP). Genotyping a MAGIC population using GBS technologies will enable us to identify marker-trait associations with high resolution.ResultsAn Upland cotton MAGIC population was developed through random-mating of 11 diverse cultivars for five generations. In this study, fiber quality data obtained from four environments and 6071 SNP markers generated via GBS and 223 microsatellite markers of 547 recombinant inbred lines (RILs) of the MAGIC population were used to conduct a genome wide association study (GWAS). By employing a mixed linear model, GWAS enabled us to identify markers significantly associated with fiber quantitative trait loci (QTL). We identified and validated one QTL cluster associated with four fiber quality traits [short fiber content (SFC), strength (STR), length (UHM) and uniformity (UI)] on chromosome A07. We further identified candidate genes related to fiber quality attributes in this region. Gene expression and amino acid substitution analysis suggested that a regeneration of bulb biogenesis 1 (GhRBB1_A07) gene is a candidate for superior fiber quality in Upland cotton. The DNA marker CFBid0004 designed from an 18 bp deletion in the coding sequence of GhRBB1_A07 in Acala Ultima is associated with the improved fiber quality in the MAGIC RILs and 105 additional commercial Upland cotton cultivars.ConclusionUsing GBS and a MAGIC population enabled more precise fiber QTL mapping in Upland cotton. The fiber QTL and associated markers identified in this study can be used to improve fiber quality through marker assisted selection or genomic selection in a cotton breeding program. Target manipulation of the GhRBB1_A07 gene through biotechnology or gene editing may potentially improve cotton fiber quality.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3249-2) contains supplementary material, which is available to authorized users.

Metabolic GWAS‐based dissection of genetic bases underlying the diversity of plant metabolism

“…However, the extremely unbalanced parental compositions might dilute the GWAS efficiency (Xiao et al ., ). To thoroughly intercross and effectively balance the contributions of all founder lines, the advanced generation intercross (MAGIC) populations of rice were established in various species (Kover et al ., ; Huang et al ., ; Bandillo et al ., ; Dell'Acqua et al ., ; Islam et al ., ). The application of NAM or MAGIC populations is largely limited, due to the requirement for extensive field and laboratory effort.…”

Molecular characterization of genetic basis of Sugarcane Yellow Leaf Virus (SCYLV) resistance in Saccharum spp. hybrid

“…Most of the mapping studies in sugarcane have used traditional molecular markers such as simple sequence repeat (SSR), restriction fragment length polymorphism (RFLP), amplified fragment length polymorphism (AFLP), random amplified polymorphic (RAPD) and diversity array technology (DArT). With the advent of next‐generation sequencing (NGS) technologies and appropriate bioinformatics software, genotype by sequencing (GBS), as a restriction enzyme‐based method, has been proven to be efficient in rapidly identifying and genotyping large numbers of single‐nucleotide polymorphism (SNP) markers in many crops both diploid (Elshire et al., ; Pace, Gardner, Romay, Ganapathysubramanian, & Lubberstedt, ; Vuong et al., ) and polyploid (Islam, Thyssen, Jenkins, & Fang, ; Islam et al., ; Poland, Brown, Sorrells, & Jannink, ). However, the GBS technology has rarely been exploited in sugarcane genotyping due to its highly heterozygosity, large genome size and lack of reference genome to facilitate downstream SNP analysis.…”

Association mapping for seed cotton yield, yield components and fibre quality traits in upland cotton (Gossypium hirsutum L.) genotypes

“…MLMs have been widely used as they consider population structure and kinship, which would ultimately control the false association to a greater extent. Many association mapping studies published to date were dedicated to study seed quality (Badigannavar & Myers, ), yield (Kantartzi & Stewart, ), fibre quality (Abdurakhmonov et al., ; Islam et al., ), maturity (Su et al., ) and biotic (Zhao, Wang, Chen, & Li, ) and abiotic stress tolerance (Saeed, Wangzhen, & Tianzhen, ; Yin‐hua et al., ) traits. We report here population structure, kinship and an average extent of genomewide LD for cotton germplasm using 23,254 informative markers from a total of 63,058 SNP markers screened.…”

“…Majority of mapping studies reported so far in cotton are based on SSRs (simple sequence repeat markers; Nie et al, 2016). To date, very few SNP-based genomewide association studies are reported in cotton (Islam et al, 2016;Su et al, 2016). Recently, 63K SNP-chip has been developed by Hulse-Kemp et al (2015) in cotton.…”