Alterations in Growth Habit to Channel End-of-Season Perennial Reserves towards Increased Yield and Reduced Regrowth after Defoliation in Upland Cotton (Gossypium hirsutum L.)

Abstract

Cotton (Gossypium spp.) is the primary source of natural textile fiber in the U.S. and a major crop in the Southeastern U.S. Despite constant efforts to increase the cotton fiber yield, the yield gain has stagnated. Therefore, we undertook a novel approach to improve the cotton fiber yield by altering its growth habit from perennial to annual. In this effort, we identified genotypes with high-expression alleles of five floral induction and meristem identity genes (FT, SOC1, FUL, LFY, and AP1) from an Upland cotton mini-core collection and crossed them in various combinations to develop cotton lines with annual growth habit, optimal flowering time, and enhanced productivity. To facilitate the characterization of genotypes with the desired combinations of stacked alleles, we identified molecular markers associated with the gene expression traits via genome-wide association analysis using a 63 K SNP Array. Over 14,500 SNPs showed polymorphism and were used for association analysis. A total of 396 markers showed associations with expression traits. Of these 396 markers, 159 were mapped to genes, 50 to untranslated regions, and 187 to random genomic regions. Biased genomic distribution of associated markers was observed where more trait-associated markers mapped to the cotton D sub-genome. Many quantitative trait loci coincided at specific genomic regions. This observation has implications as these traits could be bred together. The analysis also allowed the identification of candidate regulators of the expression patterns of these floral induction and meristem identity genes whose functions will be validated.

Development of High-Yielding Upland Cotton Genotypes with Reduced Regrowth after Defoliation Using a Combination of Molecular and Conventional Approaches

“…These genotypes were cultivated at PDREC in the same field (34 • 18 39 N 79 • 44 40 W) consecutively for three years, from 2017 to 2019. This minicore collection represents over 92% diversity of a larger collection of the upland cotton genotypes released in the USA in the past 100 years [45]. A list of 44 genotypes used in this study is presented in Table S1.…”

“…These genotypes were selected from a screen of the 44 upland cotton mini-core collection lines for the high-expression alleles of the selected cotton genes at three developmental stages from 2017-2019 using qRT-PCR (for details, see ref. [45]). Collectively, we recorded data for 45 gene expression traits, i.e., five genes and three developmental stages, for three consecutive years (5 × 3 × 3).…”

“…In this system, each individual genotype was given a point for an expression trait when it was found to express a gene at a developmental stage more than the population mean of that gene's expression in a given year. In this way, an individual genotype could receive a maximum of 45 points (5 genes × 3 developmental stages × 3 years) [45]. The genetic crosses between selected cotton genotypes with complementary expression patterns of the selected genes were made reciprocally in the field in the 2018 and 2019 growing seasons following the commonly used procedure.…”

“…With these alterations, we expect changes in the plant architecture, height, flowering time, boll number, internode length, and pre/post-harvest regrowth. To achieve this objective, we collected tissues at three developmental stages, stage 1 (S1)-10 days after sowing (DASs), stage 2 (S2)-30 DASs, and stage 3 (S3)-45 DASs, respectively, from cotyledonary leaves, immature square, and mature square, for three consecutive years from 2017 to 2019 to study expression patterns of five floral induction and meristem identity genes, FT, SOC1, LFY, AP1, and FUL and identify high-expression alleles of these genes [45]. We hypothesized that the high-expression alleles of these signal integrators and meristem identity genes would result in plants with annual growth habit exhibiting reduced to no regrowth after defoliation and enhanced yield, as the assimilates would be channeled towards fiber yield over storage in buds for regrowth.…”

“…To identify high-expression alleles of selected genes, we developed an arbitrary expression matrix, where any genotype showing an expression level more than the population mean at a developmental stage in a study year was given a point. The genotypes were sorted from high to low expression levels [45] to make genetic crosses with an aim to stack the high-expression alleles of floral induction and meristem identity genes in a single genetic background. The specific objectives of the study were to (i) stack the complementing high-expression alleles of five floral induction and meristem identity genes by genetic crossing of selected genotypes; (ii) evaluate selected lines for surrogate traits for annual growth habit; (iii) develop molecular markers for reliable screening of genotypes with reduced regrowth after defoliation.…”