Enhancing upland cotton for drought resilience, productivity and fiber quality: Comparative evaluations and genetic dissection

Authors: Ulloa, Mauricio; DE SANTIAGO, LUIS - Texas A&M University; Hulse-Kemp, Amanda; STELLLY, DAVID - Texas A&M University; BURKE, JOHN - Retired ARS Employee

Submitted to: Molecular Genetics and Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/22/2019
Publication Date: 10/16/2019
Citation: Ulloa, M., De Santiago, L., Hulse-Kemp, A.M., Stellly, D.M., Burke, J.J. 2019. Enhancing upland cotton for drought resilience, productivity and fiber quality: Comparative evaluations and genetic dissection. Molecular Genetics and Genomics. 295(1):155-176. https://doi.org/10.1007/s00438-019-01611-6.
DOI: https://doi.org/10.1007/s00438-019-01611-6

Interpretive Summary: Modern society must increase overall crop production while conserving and preserving natural resources to meet the food, fiber and energy needs of an increasing population. Producing more with diminishing water resources is an especially daunting endeavor. Genetically improving drought resilience of Upland cotton is a specific objective to meet such goals. However, the genetics that affect fiber production and quality under regular-water versus low-water or deficit irrigation field conditions is not fully understand. To facilitate genetic inferences, 10 traits were used to assess productivity and fiber quality with diverse cotton lines by scientsts from USDA-ARS (Lubbock, Texas and Stoneville, Mississippi), and Texas A&M AgriLife Research. Significant differences in these lines to response to water deficit or plant resilience were observed. Molecular analyses detected more than 150 quantitative trait locations associated with productivity and fiber quality. The identification of genomic regions associated with responses to plant stress/drought increases the possibility of using marker-assisted and omics-based selection to enhance breeding for drought resilient cultivars.

Technical Abstract: To provision the world sustainably, modern society must increase overall crop production while conserving and preserving natural resources. Producing more with diminishing water resources is an especially daunting endeavor. Towards the goal of genetically improving drought resilience of cultivated Upland cotton (Gossypium hirsutum L.), a major crop, this study addresses the genetics of differential productivity and fiber quality under regular-water (RW) versus low-water (LW) field conditions. We used 10 traits to assess resilience, including productivity (6) and fiber quality (4), for two recombinant inbred line (RIL) populations from reciprocally crossed cultivars Phytogen 72 (PHY72) and Stoneville 474 (STV474). To facilitate genetic inferences, we genotyped RILs with the CottonSNP63K array, assembled high-density linkage maps of over 7000 SNPs, and then analyzed quantitative trait variations. Analysis of variance revealed significant differences for all traits (p < 0.05) in these RIL populations. Although the LW irrigation regime significantly reduced all traits, except lint percent, the RILs exhibited a broad phenotypic spectrum of heritable differences across the water regimes. Transgressive segregation occurred among the RILs, suggesting the possibility of genetic gain through phenotypic selection for drought resilience, and perhaps through marker-based selection. Analyses revealed more than 150 quantitative trait loci (QTLs) associated with productivity and fiber quality traits (p < 0.005) on different genomic regions of the cotton genome. The MQM analysis with LOD > 3.0 detected 21 QTLs associated with productivity and 22 QTLs associated with fiber quality. For fiber traits, strong clustering and QTL associations occurred in c08 and its homeolog c24, as well as, c10, c14, and c21. Using contemporary genome sequence assemblies and bioinformatically related information, the identification of genomic regions associated with responses to plant stress/drought elevates the possibility of using marker-assisted and omics-based selection to enhance breeding for drought resilient cultivars and identifying candidate genes and networks. The heritable variation among elite bi-parental RILs for productivity and quality under field drought conditions, and their association of QTLs and thus specific genomic regions, indicate opportunities for breeding-based gains in water resource conservation, i.e., enhancing cotton's agricultural sustainability.