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ARS Home » Southeast Area » New Orleans, Louisiana » Southern Regional Research Center » Cotton Fiber Bioscience Research » Research » Publications at this Location » Publication #333421
Title: A MAGIC population-based genome-wide association study reveals functional association of GhRBB1_A07 gene with superior fiber quality in cotton

Author
item Islam, Md
item Thyssen, Gregory
item Jenkins, Johnie
item Zeng, Linghe
item Delhom, Christopher
item McCarty, Jack
item Deng, Dewayne
item Hinchliffe, Doug
item JONES, DON - Cotton, Inc
item Fang, David

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/2/2016
Publication Date: 11/9/2016
Citation: Islam, M.S., Thyssen, G.N., Jenkins, J.N., Zeng, L., Delhom, C.D., McCarty, J.C., Deng, D.D., Hinchliffe, D.J., Jones, D.C., Fang, D.D. 2016. A MAGIC population-based genome-wide association study reveals functional association of GhRBB1_A07 gene with superior fiber quality in cotton. BMC Genomics. 17:903. https://doi.org/10.1186/s12864-016-3249-2.
DOI: https://doi.org/10.1186/s12864-016-3249-2

Interpretive Summary: 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. We developed a multi-parent advanced generation inter-cross (MAGIC) population in order to break this negative correlation. Genotyping-by-sequencing (GBS) was employed to identify and genotype a large number of single nucleotide polymorphisms (SNP). In this study, fiber quality data obtained from four environments and 6,071 SNP markers generated via GBS and 224 microsatellite markers of 547 recombinant inbred lines (RILs) of the MAGIC population were used to identify markers associated with fiber quality traits. We identified and validated one cluster associated with four fiber quality traits: short fiber content, strength, length and uniformity 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 the 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. This marker is useful in a breeding program to improve fiber quality via marker-assisted selection strategy.

Technical 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 the 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 6,071 SNP markers generated via GBS and 224 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, strength, length and uniformity 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 the 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.