Genome-wide association study reveals novel quantitative trait loci and candidate genes of lint percentage in upland cotton based on the CottonSNP80K array

Deepening genomic sequences of 1081 Gossypium hirsutum accessions reveals novel SNPs and haplotypes relevant for practical breeding utility

Fiber quality is a major breeding goal in cotton, but phenotypically direct selection is often hindered. In this study, we identified fiber quality and yield related loci using GWAS based on 2.97 million SNPs obtained from 10.65× resequencing data of 1081 accessions. The results showed that 585 novel fiber loci, including two novel stable SNP peaks associated with fiber length on chromosomes At12 and Dt05 and one novel genome regions linked with fiber strength on chromosome Dt12 were identified. Furthermore, by means of gene expression analysis, GhM_A12G0090, GhM_D05G1692, GhM_D12G3135 were identified and GhM_D11G2208 function was identified in Arabidopsis. Additionally, 14 consistent and stable superior haplotypes were identified, and 25 accessions were detected as possessing these 14 superior haplotype in breeding. This study providing fundamental insight relevant to identification of genes associated with fiber quality and yield will enhance future efforts toward improvement of upland cotton.

Quantitative genomics-enabled selection for simultaneous improvement of lint yield and seed traits in cotton (Gossypium hirsutum L.)

KEY MESSAGE

A Bayesian linkage disequilibrium-based multiple-locus mixed model identified QTLs for fibre, seed and oil traits and predicted breeding worthiness of test lines, enabling their simultaneous improvement in cotton. Improving cotton seed and oil yields has become increasingly important while continuing to breed for higher lint yield. In this study, a novel Bayesian linkage disequilibrium-based multiple-locus mixed model was developed for QTL identification and genomic prediction (GP). A multi-parent population consisting of 256 recombinant inbred lines, derived from four elite cultivars with distinct combinations of traits, was used in the analysis of QTLs for lint percentage, seed index, lint index and seed oil content and their interrelations. All four traits were moderately heritable and correlated but with no large influence of genotype × environment interactions across multiple seasons. Seven to ten major QTLs were identified for each trait with many being adjacent or overlapping for different trait pairs. A fivefold cross-validation of the model indicated prediction accuracies of 0.46-0.62. GP results based on any two-season phenotypes were strongly correlated with phenotypic means of a pooled analysis of three-season experiments (r = 0.83-0.92). When used for selection of improvement in lint, seed and oil yields, GP captured 40-100% of individuals with comparable lint yields of those selected based on the three-season phenotypic results. Thus, this quantitative genomics-enabled approach can not only decipher the genomic variation underlying lint, seed and seed oil traits and their interrelations, but can provide predictions for their simultaneous improvement. We discuss future breeding strategies in cotton that will enhance the entire value of the crop, not just its fibre.

A comprehensive review on Gossypium hirsutum resistance against cotton leaf curl virus

Cotton (Gossypium hirsutum L.) is a significant fiber crop. Being a major contributor to the textile industry requires continuous care and attention. Cotton is subjected to various biotic and abiotic constraints. Among these, biotic factors including cotton leaf curl virus (CLCuV) are dominant. CLCuV is a notorious disease of cotton and is acquired, carried, and transmitted by the whitefly (Bemisia tabaci). A cotton plant affected with CLCuV may show a wide range of symptoms such as yellowing of leaves, thickening of veins, upward or downward curling, formation of enations, and stunted growth. Though there are many efforts to protect the crop from CLCuV, long-term results are not yet obtained as CLCuV strains are capable of mutating and overcoming plant resistance. However, systemic-induced resistance using a gene-based approach remained effective until new virulent strains of CLCuV (like Cotton Leaf Curl Burewala Virus and others) came into existence. Disease control by biological means and the development of CLCuV-resistant cotton varieties are in progress. In this review, we first discussed in detail the evolution of cotton and CLCuV strains, the transmission mechanism of CLCuV, the genetic architecture of CLCuV vectors, and the use of pathogen and nonpathogen-based approaches to control CLCuD. Next, we delineate the uses of cutting-edge technologies like genome editing (with a special focus on CRISPR-Cas), next-generation technologies, and their application in cotton genomics and speed breeding to develop CLCuD resistant cotton germplasm in a short time. Finally, we delve into the current obstacles related to cotton genome editing and explore forthcoming pathways for enhancing precision in genome editing through the utilization of advanced genome editing technologies. These endeavors aim to enhance cotton's resilience against CLCuD.

Dissecting the major genetic components underlying cotton lint development

Numerous genetic loci and several functionally characterized genes have been linked to determination of lint percentage (lint%), one of the most important cotton yield components, but we still know little about the major genetic components underlying lint%. Here, we first linked the genetic loci containing MYB25-like_At and HD1_At to the fiberless seed trait of 'SL1-7-1' and found that MYB25-like_At and HD1_At were very lowly expressed in 'SL1-7-1' ovules during fiber initiation. We then dissected the genetic components involved in determination of lint% using segregating populations derived from crosses of fuzzless mutants and intermediate segregants with different lint%, which not only confirmed the HD1_At locus but identified the HD1_Dt locus as being the major genetic components contributing to fiber initiation and lint%. The segregating populations also allowed us to evaluate the relative contributions of MYB25-like_At, MYB25-like_Dt, HD1_At, and HD1_Dt to lint%. Haplotype analysis of an Upland cotton (Gossypium hirsutum) population with 723 accessions (including 81 fuzzless seed accessions) showed that lint% of the accessions with the LP allele (higher lint%) at MYB25-like_At, MYB25-like_Dt, or HD1_At was significantly higher than that with the lp allele (lower lint%). The lint% of the Upland cotton accessions with 3 or 4 LP alleles at MYB25-like and HD1 was significantly higher than that with 2 LP alleles. The results prompted us to propose a strategy for breeding high-yielding cotton varieties, i.e. pyramiding the LP alleles of MYB25-like and HD1 with new lint% LP alleles without negative impact on seed size and fiber quality.

Genetic diversity and population structure analyses and genome-wide association studies of photoperiod sensitivity in cotton (Gossypium hirsutum L.)

KEY MESSAGE

Genetic diversity and population structure analyses showed progressively narrowed diversity in US Upland cotton compared to land races. GWAS identified genomic regions and candidate genes for photoperiod sensitivity in cotton. Six hundred fifty-seven accessions that included elite cotton germplasm (DIV panel), lines of a public cotton breeding program (FB panel), and tropical landrace accessions (TLA panel) of Gossypium hirsutum L. were genotyped with cottonSNP63K array and phenotyped for photoperiod sensitivity under long day-length conditions. The genetic diversity analysis using 26,952 polymorphic SNPs indicated a progressively narrowed diversity from the landraces (0.230) to the DIV panel accessions (0.195) and FB panel (0.116). Structure analysis in the US germplasm identified seven subpopulations representing all four major regions of the US cotton belt. Three subpopulations were identified within the landrace accessions. The highest fixation index (FST) of 0.65 was found between landrace accessions of Guatemala and the Plains-type cultivars from Southwest cotton region while the lowest FST values were between the germplasms of Mid-South and Southeastern regions. Genome wide association studies (GWAS) of photoperiod response using 600 phenotyped accessions identified 14 marker trait associations spread across eight Upland cotton chromosomes. Six of these marker trait associations, on four chromosomes (A10, D04, D05, and D06), showed significant epistatic interactions. Targeted genomic analysis identified regions with 19 candidate genes including Transcription factor Vascular Plant One-Zinc Finger 1 (VOZ1) and Protein Photoperiod-Independent Early Flowering 1 (PIE1) genes. Genetic diversity and genome wide analyses of photoperiod sensitivity in diverse cotton germplasms will enable the use of genomic tools to systematically utilize the tropical germplasm and its beneficial alleles for broadening the genetic base in Upland cotton.

Genetic dissection of lint percentage in short-season cotton using combined QTL mapping and RNA-seq

KEY MESSAGE

In total, 17 QTLs for lint percentage in short-season cotton, including three stable QTLs, were detected. Twenty-eight differentially expressed genes located within the stable QTLs were identified, and two genes were validated by qRT-PCR. The breeding and use of short-season cotton have significant values in addressing the question of occupying farmlands with either cotton or cereals. However, the fiber yields of short-season cotton varieties are significantly lower than those of middle- and late-maturing varieties. How to effectively improve the fiber yield of short-season cotton has become a focus of cotton research. Here, a high-density genetic map was constructed using genome resequencing and an RIL population generated from the hybridization of two short-season cotton accessions, Dong3 and Dong4. The map contained 4960 bin markers across the 26 cotton chromosomes and spanned 3971.08 cM, with an average distance of 0.80 cM between adjacent markers. Based on the genetic map, quantitative trait locus (QTL) mapping for lint percentage (LP, %), an important yield component trait, was performed. In total, 17 QTLs for LP, including three stable QTLs, qLP-A02, qLP-D04, and qLP-D12, were detected. Three out of 11 non-redundant QTLs overlapped with previously reported QTLs, whereas the other eight were novel QTLs. A total of 28 differentially expressed genes associated with the three stable QTLs were identified using RNA-seq of ovules and fibers at different seed developmental stages from the parental materials. The two genes, Ghir_A02G017640 and Ghir_A02G018500, may be related to LP as determined by further qRT-PCR validation. This study provides useful information for the genetic dissection of LP and promotes the molecular breeding of short-season cotton.

Lint percentage and boll weight QTLs in three excellent upland cotton (Gossypium hirsutum): ZR014121, CCRI60, and EZ60

BACKGROUND

Upland cotton (Gossypium hirsutum L.) is the most economically important species in the cotton genus (Gossypium spp.). Enhancing the cotton yield is a major goal in cotton breeding programs. Lint percentage (LP) and boll weight (BW) are the two most important components of cotton lint yield. The identification of stable and effective quantitative trait loci (QTLs) will aid the molecular breeding of cotton cultivars with high yield.

RESULTS

Genotyping by target sequencing (GBTS) and genome-wide association study (GWAS) with 3VmrMLM were used to identify LP and BW related QTLs from two recombinant inbred line (RIL) populations derived from high lint yield and fiber quality lines (ZR014121, CCRI60 and EZ60). The average call rate of a single locus was 94.35%, and the average call rate of an individual was 92.10% in GBTS. A total of 100 QTLs were identified; 22 of them were overlapping with the reported QTLs, and 78 were novel QTLs. Of the 100 QTLs, 51 QTLs were for LP, and they explained 0.29-9.96% of the phenotypic variation; 49 QTLs were for BW, and they explained 0.41-6.31% of the phenotypic variation. One QTL (qBW-E-A10-1, qBW-C-A10-1) was identified in both populations. Six key QTLs were identified in multiple-environments; three were for LP, and three were for BW. A total of 108 candidate genes were identified in the regions of the six key QTLs. Several candidate genes were positively related to the developments of LP and BW, such as genes involved in gene transcription, protein synthesis, calcium signaling, carbon metabolism, and biosynthesis of secondary metabolites. Seven major candidate genes were predicted to form a co-expression network. Six significantly highly expressed candidate genes of the six QTLs after anthesis were the key genes regulating LP and BW and affecting cotton yield formation.

CONCLUSIONS

A total of 100 stable QTLs for LP and BW in upland cotton were identified in this study; these QTLs could be used in cotton molecular breeding programs. Putative candidate genes of the six key QTLs were identified; this result provided clues for future studies on the mechanisms of LP and BW developments.

Sequence Characteristics and Expression Analysis of the Gene Encoding Sedoheptulose-1,7-Bisphosphatase, an Important Calvin Cycle Enzyme in Upland Cotton (Gossypium hirsutum L.)

Sedoheptulose-1,7-bisphosphatase (SBPase, EC 3.1.3.37) is a key enzyme in the plant Calvin cycle and one of the main rate-limiting enzymes in the plant photosynthesis pathway. Many studies have demonstrated that the SBPase gene plays an important role in plant photosynthetic efficiency, yield, and stress responses; however, few studies have been conducted on the function and expression of the GhSBPase gene in upland cotton. In this study, our results showed that the coding sequence (CDS) of GhSBPase gene was 1182 bp, encoding a protein with 393 amino acids. The GhSBPase protein had adenosine monophosphate (AMP) binding site and a FIG (FBPase/IMPase/glpX) domain, and had six Cys residues and a CGGT(A/Q)C motif that were involved in redox regulation in plants. Evolutionarily, the GhSBPase protein clustered into the dicotyledon subgroup and was most closely related to the tomato SlSBPase protein. Western-blot analysis further indicated that the GhSBPase gene was indeed the gene encoding the SBPase protein in upland cotton. The GhSBPase protein was localized in chloroplast, which was consistent with its function as a key enzyme in photosynthesis. The GhSBPase gene was specifically highly expressed in leaves, and its expression level was significantly lower in a yellow-green leaf mutant than in the wild type. Moreover, the GhSBPase expression was in response to drought, salt, high- and low-temperature stress, and exhibits different expression patterns. The GhSBPase promoter had the cis-acting elements in response to abiotic stress, phytohormone, and light. In addition, the GhSBPase expression was positively correlated with the chlorophyll fluorescence parameters, suggesting that changes in the expression of the GhSBPase had potential applicability in breeding for enhanced cotton photosynthetic efficiency. These results will help to understand the function of the GhSBPase gene in photosynthesis and the adaptability of plants to external stress and provide important gene information for the high-yield breeding of crops in the future.