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

Abstract

Background: Cotton 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.

Results: An 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.

Conclusion: Using 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.

Keywords: Cotton; Fiber quality; Genome wide association study; Genotyping-by-sequencing; Multi parent advanced generation inter-cross.

Fig. 1

Breeding scheme of Upland cotton MAGIC population. Recombinant inbred lines (RILs) were developed according to the crossing scheme as below and 55 sub-families (10 shown here) were established. Individual colors represents the 11 parents (AU - Acala Ultima, TP - Tamcot Pyramid, C315 - Coker 315, ST825 - Stoneville 825, FM966 – Fibermax 966, M240 - M-240RNR, HS26 - Paymaster HS-26, DP90 - Deltapine Acala 90, SG747 – Suregrow 747, PSC355 – Phytogen 355, ST474 – Stoneville 474)

Fig. 2

Linkage disequilibrium (LD) decay across all chromosomes. a A_t sub-genome, b D_t sub-genome

Fig. 3

Manhattan plots generated from GAPIT software for six fiber quality traits, a Elongation (ELO), b Micronaire (MIC), c Short fiber content (SFC), d Fiber strength (STR), e Upper half mean (UHM) fiber length, and f Uniformity (UI). The negative log₁₀ transformed p values were plotted against the marker positions on the physical map of each of the 26 Upland cotton chromosome. The significant thresholds (p = 0.01 and 0.0001) are indicated by the purple and green horizontal dot line, respectively

Fig. 4

The effect of two marker loci selection on fiber elongation of RILs. RILs were divided into four groups based on the allele combinations at two marker loci that flanked a significant ELO QTL

Fig. 5

The effect of two marker loci selection on four fiber quality traits of RILs. a Short fiber content (SFC), b Fiber bundle strength (STR), c Fiber length (UHM), and d Uniformity (UI). RILs were divided into four groups based on the allele combinations at two marker loci that flanked a significant QTL of the respective trait

Fig. 6

RT-qPCR gene expression analyses of gene Gh_A07G2049 (GhRBB1_A07) during fiber development between Acala Ultima (AU) and Tamcot Pyramid (TP)

Fig. 7

The correlation between the InDel marker CFBid0004 and fiber quality traits in MAGIC RILs and NCVT cultivars. Based on the marker genotypes, all 550 RILs of MAGIC population (a-d) and 105 Upland cotton cultivars (e and f) were divided into two groups: 1) RILs or cultivars carrying 147 bp allele and 2) the remaining RILs or cultivars containing 165 bp. The significant mean fiber traits of the genotype having 147 and 165 bp allele were shown in red and black circle, respectively