Genetic and transcriptomic dissection of the fiber length trait from a cotton (Gossypium hirsutum L.) MAGIC population

Authors: Naoumkina, Marina; Thyssen, Gregory; Fang, David; Jenkins, Johnie; McCarty, Jack; Florane, Christopher

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/2/2019
Publication Date: 2/6/2019
Citation: Naoumkina, M.A., Thyssen, G.N., Fang, D.D., Jenkins, J.N., McCarty, J.C., Florane, C.B. 2019. Genetic and transcriptomic dissection of the fiber length trait from a cotton (Gossypium hirsutum L.) MAGIC population. BMC Genomics. 20:112. https://doi.org/10.1186/s12864-019-5427-5.
DOI: https://doi.org/10.1186/s12864-019-5427-5

Interpretive Summary: Cotton fiber length is a key determinant of fiber quality for the textile industry. Genetic improvement of cotton fiber length without reducing fiber yield is one of the major goals for breeding upland cotton. However, genetic improvement of cotton fiber length by breeding is difficult due to narrow genetic diversity of modern cotton cultivars. A population developed through random-mating of multiple various parents provides an excellent diverse genetic resource for identification of genes contributed to fiber quality traits. In our study we used such population for identification of genes controlling fiber length. We found a genomic segment on chromosome D11 controlling fiber length in the population. We evaluated the differences in gene expression level between the longest and shortest fiber lines in the population. We found that different functional categories of genes were regulated in selected lines during fiber development. Also we found a possible candidate gene on chromosome D11 controlling fiber length.

Technical Abstract: Background: Improving cotton fiber length without reducing yield is one of the major goals for cotton breeding. However, genetic improvement of cotton fiber length by breeding has been a challenge due to the narrow genetic diversity of modern cotton cultivars and negative correlations between fiber quality and yield traits. A multi-parent advanced generation inter-cross (MAGIC) population developed through random mating provides an excellent genetic resource that allows quantitative trait loci (QTL) and causal genes to be identified. Results: An Upland cotton MAGIC population, consisting of 550 recombinant inbred lines (RILs) derived from eleven different cultivars, was used to identify fiber length QTLs and potential genes that contribute to longer fibers. A genome wide association study (GWAS) identified a cluster of single nucleotide polymorphisms (SNPs) on chromosome (Chr.) D11 that is significantly associated with fiber length. Further evaluation of the Chr. D11 genomic region among lines of the MAGIC population detected that 90% of RILs have a D11 haplotype similar to the reference TM-1 genome (D11-ref), whereas 10% of RILs inherited an alternative haplotype from one of the parents (D11-alt). The average length of fibers of D11-alt RILs was significantly shorter comparing to D11-ref RILs, suggesting that alleles in the D11-alt haplotype contributed to the inferior fiber quality. RNAseq analysis of the longest and shortest fiber length RILs from D11-ref and D11-alt populations identified 949 significantly differentially expressed genes (DEGs). Gene set enrichment analysis revealed that different functional categories of genes were over-represented during fiber elongation between the four selected RILs. We found 12 genes possessing non-synonymous SNPs (nsSNPs) significantly associated with the fiber length. In close proximity to the Chr. D11 fiber length QTL, we identified an auxin-responsive GH3 gene with a significantly down regulated expression level in one of the longest fiber length RILs suggesting it could be a potential candidate involved in regulation of cotton fiber cell elongation. Conclusion: The results of this study provide insights into molecular aspects of genetic variation in fiber length and suggests candidate genes for genetic manipulation for cotton improvement.