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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 #353548

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

item Naoumkina, Marina
item Thyssen, Gregory
item Fang, David
item Jenkins, Johnie
item McCarty, Jack
item Florane, Christopher

Submitted to: American Society of Plant Biologists Annual Meeting
Publication Type: Abstract Only
Publication Acceptance Date: 5/22/2018
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Cotton fiber length is a key determinant of fiber quality for the textile industry. 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 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 diverse genetic resource that allow quantitative trait loci (QTL) and causal genes to be identified. In this study we used an Upland cotton MAGIC population derived from 11 different cultivars through 6 cycles of random mating to find fiber length QTL and potential genes that contribute to longer fiber. A genome wide association analysis of half million SNPs (obtained by genomic sequencing of 550 recombinant inbred lines (RILs) from the MAGIC population) with fiber length of these RILs identified a cluster of SNPs on chromosome D11 significantly associated with a fiber length QTL. Further evaluation of D11 genomic sequence region among 550 RILs detected that 90% of RILs have D11-0 chromosomal segment similar to reference TM-1 genome, whereas 10% of RILs inherited D11-1 chromosomal segment from one of the parents. The average length of fibers of D11-1 RILs was significantly shorter comparing to D11-0 RILs, suggesting that alleles from D11-1 chromosomal region contributed to worse fiber properties. To get insights into molecular aspects of genetic diversity of fiber length we performed SNPs and RNAseq analysis of the longest and shortest in fiber length RILs from D11-0 and D11-1 populations. Developing cotton fibers at 8 days post anthesis (DPA) were used for RNAseq analysis. We found 949 genes that were significantly differentially expressed between four RILs in six comparisons. Quantities of differentially expressed genes between comparisons were relatively similar, from smallest 328 to largest 395 genes. However, gene set enrichment analysis revealed that different functional categories of genes were activated at 8 DPA during fiber elongation in four RILs. In the close proximity from cluster of SNPs significantly associated with fiber length QTL on D11 chromosome we found an auxin responsive gene with expression level significantly down-regulated in one of the longest fiber RILs suggesting it could be a promising candidate involved in regulation of fiber elongation.