Traits In Cotton Research Articles

Reversing anther thermotolerance by manipulating the cis-elements in the promoter of a high-temperature upregulated gene Casein Kinase I in upland cotton.

High temperature (HT) stress causes male sterility, leading to reduced upland cotton yield. Previously, we identified a key gene, Casein Kinase I (GhCKI), that negatively regulates male fertility in upland cotton under HT. However, conventional genetic manipulations of GhCKI would result in male sterility, hindering its utilization in breeding programs. Here, we engineered quantitative variation for anther thermotolerance-related traits in upland cotton by creating weak promoter alleles of GhCKI genes, using CRISPR/Cas9 and CRISPR/Cpf1 genome editing. Then, we screened and identified two new upland cotton plant lines exhibiting a HT-tolerant phenotype with edited GhCKI promoters, and characterized their corresponding heat-tolerant allelic genotypes. Further research revealed that the primary reason for the HT tolerance of the GhCKI promoter editing mutants is that the trans-acting factors GhMYB73 and GhMYB4, which positively regulate GhCKI expression under HT, failed to bind and activate the expression of GhCKI. Overall, our study not only provides a rapid strategy to generate new beneficial alleles but also offers novel germplasm resources and molecular insights for crop HT tolerance breeding.

Inheritance of yield and fiber length in hybrids cotton of the first generation F1

The patterns of inheritance and variability of economically valuable traits in cotton, manifestations of heterosis, as well as its preservation in hybrid populations with a high inheritance potential during intraspecific and genotypically distant hybridization were determined. Thus, in order to obtain heterosis hybrid combinations in Fl for the “fiber yield” trait, cotton varieties with the same or closele related indicators of this trait were involved in crossing (UF0800038 K 113 / UF0800040 K 111, UF0800038 K 113 /UF0800256 0212). Dominance of one of the parent forms according to the trait “fiber length” in F1 plants is manifested in hybrids that differ sharply in terms of indicators. An intermediate type of trait inheritance was observed in hybrids genotypically close and geographically distant in origin. When studying the variability and inheritance of the trait “fiber length” in parental varieties and their F1 hybrids, it was found that positive overdominance or positive heterosis for the fiber length trait was observed in hybrids with different genotypes and in geographically distant forms. Negative superdominance based on fiber length, i.e. negative heterosis, was found in hybrids with different genotypes and indicators, as well as in samples geographically distant in origin. In general, analyzing the fiber length inheritance data, it can be concluded that the F1 hybrid combinations mainly showed negative and positive overdominance. Therefore, it can be argued that the fiber length in F1 hybrids is mainly regulated by dominant genes.

Genetic analysis of F1 and F2 generations for early mature, yield and fibre traits in upland cotton (Gosypium hirsutum L.)

Genetic analysis of F1 and F2 generations for early mature, yield and fibre traits in upland cotton (Gosypium hirsutum L.)

Genome-Wide Identification and Analysis of the MYC Gene Family in Cotton: Evolution and Expression Profiles During Normal Growth and Stress Response.

The gene family of myelomatosis (MYC), serving as a transcription factor in the jasmonate (JA) signaling pathway, displays a significant level of conservation across diverse animal and plant species. Cotton is the most widely used plant for fiber production. Nevertheless, there is a paucity of literature reporting on the members of MYCs and how they respond to biotic stresses in cotton. Bioinformatics analysis was used to mine the MYC gene family in cotton based on InterPro, cottongen, etc. Results: The gene structure, conserved motifs, and upstream open reading frames of 32 GhMYCs in Gossypium hirsutum were identified. Moreover, it was anticipated that the GT1-motif is the most abundant in GhMYCs, indicating that the GT1-motif plays a significant role in light-responsive GhMYCs. The expression patterns of GhMYCs under biotic stresses including V. dahliae and Aphid gossypii were evaluated, suggesting that GhMYCs in class-1 and -3 GhMYCs, which function as negative regulators, are involved in resistance to verticillium wilt and aphids. The class-3 GhMYCs genes were found to be mostly expressed in female tissues. Interestingly, it was also determined that the homeologous expression bias within GhMYCs in cotton was uncovered, and results showed that the gene expression of class-1A and class-2 GhMYCs in the Dt sub-genome may have a direct impact on gene function. This study provides a research direction for researchers and breeders to enhance cotton traits through manipulating individual or multiple homeologs, which laid a foundation for further study of the molecular characteristics and biological functions of GhMYC gene.

Nitrogen nutrition for cotton in a semi-arid environment

Abstract Nitrogen (N) is the most significant nutrient affecting crop growth and development for all types of crops, except legumes. The goal of this study was to optimize the N level for cotton grown in a semi-arid environment to enhance growth and development, determine N status, and increase seed cotton yield and biomass. Two independent field experiments each three years in duration were conducted, from 2007 to 2009 (Exp.-I) and 2018 to 2020 (Exp.-II). Experiments were laid out in a randomized complete block design with three replicates. The N treatments in Exp.-I were comprised of 0, 40, 80, 120, 160, 200 and 240 kg N/ha, while treatments in Exp.-II were comprised of 0, 70, 140, 210 and 280 kg N/ha. A wide range of data sets for cotton traits were recorded, including canopy height, leaf area index, the N status of the leaf and stem, seed cotton yield and time-series biomass data. The higher N rates 240 and 280 kg N/ha performed better for all these traits. However, the highest leaf N contents were recorded for 210 kg N/ha. Based on these results, it is suggested that under semi-arid conditions, slightly higher rates than optimum or recommended N rates could be applied as a strategy by cotton growers for a higher seed cotton yield. The findings of this study may also increase profitability in other cotton-growing areas that have similar weather conditions.

Transcriptome Analysis Reveals Key Pathways and Genes Involved in Lodging Resistance of Upland Cotton

Lodging resistance is one of the most important traits of machine-picked cotton. Lodging directly affects the cotton yield, quality and mechanical harvesting effect. However, there are only a few reports on the lodging resistance of cotton. In this study, the morphological and physiological characteristics and transcriptome of two upland cotton varieties with different lodging resistance were compared. The results showed that the stem strength; the contents of lignin, soluble sugar and cellulose; and the activities of several lignin biosynthesis-related enzymes of the lodging-resistant variety M153 were significantly higher than those of the lodging-susceptible variety M5330. Transcriptomic analysis showed that the expression level of several genes related to lignin, cellulose, starch and sucrose synthesis, and photosynthesis were significantly up-regulated in the lodging-resistant variety M153, which was consistent with the content determination results of lignin, cellulose and soluble sugar. Silencing two lignin biosynthesis-related genes (GhPAL and Gh4CL) in cotton via VIGS (Virus-Induced Gene Silencing) resulted in reduced lignin content and decreased lodging resistance in cotton. These results suggested that lignin, cellulose and soluble sugar contents were positively correlated with the lodging resistance of cotton, and lignin, cellulose and soluble sugar biosynthesis-related genes can be used as potential targets for improving the lodging resistance of cotton. These findings provide a theoretical basis for the cultivation of cotton varieties with strong lodging resistance in the future.

Revealing insights into Bemisia tabaci dynamics: natural enemy communities and population traits in Bt and non-Bt cotton

Revealing insights into Bemisia tabaci dynamics: natural enemy communities and population traits in Bt and non-Bt cotton

BSA-seq and transcriptome analysis reveal GhDSA05 as a candidate gene responsible for sensitivity to defoliants in Gossypium hirsutum L.

With the development of machine-harvested cotton, the application of defoliants is a key technology that can promote defoliation and reduce impurities in cotton fibers. Therefore, sensitivity to defoliants is a very important trait in machine-harvested cotton. In this study, to uncover the genetic basis of defoliant sensitivity in cotton, bulked segregant analysis by sequencing was used with a F2 population derived from Xinluzao 57 (XLZ57, defoliant sensitive) and Nan 2 (N2, defoliant insensitive) to mapped the quantitative trait locus (QTL) to a 3.66-Mb interval at chromosome A05. Then, 284 F2 individuals were used to validate and narrow the QTL to a 1.6-Mb interval and was named qSD-A05. To identify the candidate genes, dynamic transcriptome analysis of the abscission zone (AZ) in XLZ57 and N2 after defoliant treatment was performed. A total of 132 and 142 common differentially expressed genes (DEGs) were identified at all time points in N2 and XLZ57, respectively, and were enriched in the defense response pathway and abscisic acid-activated signaling pathway. More importantly, 15 DEGs were identified in the qSD-A05 interval, among which, Ghi_A05G23601 was significantly upregulated after defoliant treatment. There were multiple variants between N2 and XLZ57, including missense and frameshift mutations. Therefore, Ghi_A05G23601 was regarded as the key candidate gene and was named GhDSA05, which encodes a Facilitator superfamily transporter protein. To verify the function of GhDSA05, virus-induced gene silencing was performed, which showed that the GhDSA05-silenced plants exhibited decreased defoliant sensitivity. Additionally, the expression of organ abscission-related genes was downregulated in the GhDSA05-silenced plants. In summary, GhDSA05 positively regulates the formation of AZ under defoliant treatment and promotes leaf abscission in cotton. The results of this study not only enhance our knowledge of the defoliation mechanism of cotton but also provide a target for the genetic improvement of defoliant sensitivity.

Stability analysis for yield-associated traits in desi cotton (Gossypium arboreum) genotypes

Stability analysis for yield-associated traits in desi cotton (Gossypium arboreum) genotypes

Polygenic Genetic Analysis of Principal Genes for Yield Traits in Land Cotton

Objective: Yield traits are crucial for cotton breeding. Analyzing the yield traits of terrestrial cotton and exploring their genetic mechanisms through a primary gene + multigene hybrid genetic model provide a theoretical basis for selecting high-quality cotton varieties and identifying associated molecular markers. Methods: Completing the construction of the six populations (P1, P2, F1, F2, B1, B2) using Xinluzhong 37 as the female parent and Xinluzhong 51 as the male parent. Six yield traits were assessed: single boll weight, boll number per plant, lint yield per plant, seed cotton per plant, lint percentage, and seed index. Data were tested for normal distribution, and the inheritance patterns of yield traits were analyzed through combined primary gene + polygenic analysis. Results: The coefficients of variation for the six yield traits ranged from 37.368% to 53.905%, 33.335% to 58.524%, 34.132% to 57.686%, 8.721% to 12.808%, 1.842% to 6.283%, and 8.783% to 12.580%, respectively. These traits displayed either normal or skewed normal distributions. The optimal genetic model for single boll weight and seed index was PG-ADI, while MX2-ADI-AD best fit the traits of boll number per plant and lint percentage. For lint yield per plant and seed cotton per plant, the 2MG-ADI model was optimal. The polygenic heritability for single boll weight was 29.58%; for boll number per plant, main gene heritability was 25.19%, with 0% heritability for polygenes; for lint yield per plant, the heritability of the main gene was 23.47%. For seed cotton per plant, the heritability of main genes was 15.38%, with lint percentage showing 63.25% heritability for main genes and 0.08% for polygenes, and seed index with 45.93% heritability due to polygenes. Overall, single boll weight and seed index were predominantly polygenic, while boll number per plant and lint percentage were largely controlled by main gene inheritance. The inheritance of lint yield per plant and seed cotton per plant was also primarily governed by main genes.

Association of GhGeBP genes with fiber quality and early maturity related traits in upland cotton

Transcription Factors (TFs) are key regulators of how plants grow and develop. Among the diverse TF families, the Glabrous-enhancer binding protein (GeBP) family plays a key role in trichome initiation and leaf development. The specific roles of GeBP TFs in plants remain largely unexplored, although GeBP transcription factors play important roles in plants. This study identified 16 GhGeBP genes in Gossypium hirsutum, ranging from 534 bp (GhGeBP14) to 1560 bp (GhGeBP2). Phylogenetic analysis grouped 16 GhGeBP genes clustered into three subgroups, unevenly distributed across 14 chromosomes. Analysis of the cis-acting elements revealed 408 motifs in the 2 kb upstream regions of the promoters, including stress-responsive, phytohormone-responsive, and light-responsive elements. Tissue-specific expression analysis showed 8 GhGeBP genes were highly expressed across all tissues, while GhGeBP4 and GhGeBP12 were down-regulated under conditions of drought, salt, cold, and heat stress. A genome-wide association study (GWAS) identified GhGeBP4 was associated with fiber micronaire (FM) and fiber strength (FS), while GhGeBP9 was linked to the node of the first fruiting branch (NFFB) and flowering time (FT). Haplotype analysis revealed that GhGeBP4-HAP2 exhibited higher fiber quality traits, while GhGeBP9-HAP2 was associated with early maturity. The results of this study offer significant insights that are worthy of further investigation into the role of the GhGeBP gene family in G. hirsutum and promising targets for marker-assisted selection strategies in cotton breeding programs, particularly for improving fiber quality and early maturity traits.

Studies on heterosis and combining ability analysis for yield, yield contributing and fibre quality traits in BT cotton (BG I) (Gossypium hirsutum L.)

Studies on heterosis and combining ability analysis for yield, yield contributing and fibre quality traits in BT cotton (BG I) (Gossypium hirsutum L.)

Evaluating the Influence of Legume and Cereal Intercropping on Bt Cotton Traits in Rainfed Conditions

This study investigates how various intercropping systems involving cereals and legumes affect the phenotypic characteristics of Bt cotton. Understanding that intercropping can improve agricultural sustainability and production, we grew Bt cotton alongside various cereal and leguminous crops in several field tests. The study aimed to evaluate the effects of different cotton based intercropping systems under rainfed conditions on important phenotypic characteristics of cotton, including dry matter accumulation, crop growth rate (CGR), relative growth rate (RGR) and boll weight in black calcareous soil under rainfed conditions. The experiment conducted at Junagadh Agricultural University, Junagadh, Gujarat during kharif 2022-23 and 2023-24 with randomized block design with fifteen treatments, involving sole and intercropping systems of groundnut, sunflower, pearl millet, maize and soybean with cotton in 1:1 row proportion. According to our research, intercropping legumes like green gram, black gram and groundnut significantly improved cotton phenotypic characteristics as compare to other intercropping systems by increasing soil fertility and lowering insect burden. Dry matter per plant at 60, 90 DAS, at harvest and average boll weight were found significantly higher under sole cotton except 30 DAS during both the years of experimentation and in pooled results. Among different intercropping systems, the cotton + green gram (T14) intercropping recorded the highest dry matter, CGR and average boll weight while the lowest was recorded with the cotton + maize (T12) intercropping system. Overall, the findings show that while cereal-based systems necessitate careful management to balance competition and resource consumption, incorporating legumes into Bt cotton agriculture can provide significant agronomic benefits, including higher growth and yield. This study emphasises how crucial it is to choose the right intercrops in order to maximise the productivity and efficiency of Bt cotton systems.

Genome-wide association study of fiber quality traits in US upland cotton (Gossypium hirsutum L.).

A GWAS in an elite diversity panel, evaluated across 10 environments, identified genomic regions regulating six fiber quality traits, facilitating genomics-assisted breeding and gene discovery in upland cotton. In this study, an elite diversity panel of 348 upland cotton accessions was evaluated in 10 environments across the US Cotton Belt and genotyped with the cottonSNP63K array, for a genome-wide association study of six fiber quality traits. All fiber quality traits, upper half mean length (UHML: mm), fiber strength (FS: gtex-1), fiber uniformity (FU: %), fiber elongation (FE: %), micronaire (MIC) and short fiber content (SFC: %), showed high broad-sense heritability (> 60%). All traits except FE showed high genomic heritability. UHML, FS and FU were all positively correlated with each other and negatively correlated with FE, MIC and SFC. GWAS of these six traits identified 380 significant marker-trait associations (MTAs) including 143 MTAs on 30 genomic regions. These 30 genomic regions included MTAs identified in at least three environments, and 23 of them were novel associations. Phenotypic variation explained for the MTAs in these 30 genomic regions ranged from 6.68 to 11.42%. Most of the fiber quality-associated genomic regions were mapped in the D-subgenome. Further, this study confirmed the pleiotropic region on chromosome D11 (UHML, FS and FU) and identified novel co-localized regions on D04 (FU, SFC), D05 (UHML, FU, and D06 UHML, FU). Marker haplotype analysis identified superior combinations of fiber quality-associated genomic regions with high trait values (UHML = 32.34mm; FS = 32.73gtex-1; FE = 6.75%). Genomic analyses of traits, haplotype combinations and candidate gene information described in the current study could help leverage genetic diversity for targeted genetic improvement and gene discovery for fiber quality traits in cotton.

Integrating RTM-GWAS and meta‑QTL data revealed genomic regions and candidate genes associated with the first fruit branch node and its height in upland cotton.

Two genomic regions associated with FFBN and HFFBN and a potential regulatory gene (GhE6) of HFFBN were identified through the integration of RTM-GWAS and meta‑QTL analyses. Abstract The first fruit branch node (FFBN) and the height of the first fruit branch node (HFFBN) are two important traits that are related to plant architecture and early maturation in upland cotton. Several studies have been conducted to elucidate the genetic basis of these traits in cotton using biparental and natural populations. In this study, by using 9,244 SNP linkage disequilibrium block (SNPLDB) loci from 315 upland cotton accessions, we carried out restricted two-stage multilocus and multiallele genome-wide association studies (RTM-GWASs) and identified promising haplotypes/alleles of the four stable and true major SNPLDB loci that were significantly associated with FFBN and HFFBN. Additionally, a meta-quantitative trait locus (MQTL) analysis was conducted on 274 original QTLs that were reported in 27 studies, and 40 MQTLs associated with FFBN and HFFBN were identified. Through the integration of the RTM-GWAS and meta‑QTL analyses, two stable and true major SNPLDBs (LDB_5_15144433 and LDB_16_37952328) that were distributed in the two MQTLs were identified. Ultimately, 142 genes in the two genomic regions were annotated, and three candidate genes associated with FFBN and HFFBN were identified in the genomic region (A05:14.64-15.64Mb) via RNA-Seq and qRT‒PCR. The results of virus-induced gene silencing (VIGS) experiments indicated that GhE6 was a key gene related to HFFBN and that GhDRM1 and GhGES were important genes associated with early flowering in upland cotton. These findings will aid in the future identification of molecular markers and genetic resources for developing elite early-maturing cultivars with ideal plant characteristics.

GhSBI1, a CUP-SHAPED COTYLEDON 2 homologue, modulates branch internode elongation in cotton.

Branch length is an important plant architecture trait in cotton (Gossypium) breeding. Development of cultivars with short branch has been proposed as a main object to enhance cotton yield potential, because they are suitable for high planting density. Here, we report the molecular cloning and characterization of a semi-dominant quantitative trait locus, Short Branch Internode 1(GhSBI1), which encodes a NAC transcription factor homologous to CUP-SHAPED COTYLEDON 2 (CUC2) and is regulated by microRNA ghr-miR164. We demonstrate that a point mutation found in sbi1 mutants perturbs ghr-miR164-directed regulation of GhSBI1, resulting in an increased expression level of GhSBI1. The sbi1 mutant was sensitive to exogenous gibberellic acid (GA) treatments. Overexpression of GhSBI1 inhibited branch internode elongation and led to the decreased levels of bioactive GAs. In addition, gene knockout analysis showed that GhSBI1 is required for the maintenance of the boundaries of multiple tissues in cotton. Transcriptome analysis revealed that overexpression of GhSBI1 affects the expression of plant hormone signalling-, axillary meristems initiation-, and abiotic stress response-related genes. GhSBI1 interacted with GAIs, the DELLA repressors of GA signalling. GhSBI1 represses expression of GA signalling- and cell elongation-related genes by directly targeting their promoters. Our work thus provides new insights into the molecular mechanisms for branch length and paves the way for the development of elite cultivars with suitable plant architecture in cotton.

Expression profile analysis of cotton fiber secondary cell wall thickening stage.

To determine the genes associated with the fiber strength trait in cotton, three different cotton cultivars were selected: Sea Island cotton (Xinhai 32, with hyper-long fibers labeled as HL), and upland cotton (17-24, with long fibers labeled as L, and 62-33, with short fibers labeled as S). These cultivars were chosen to assess fiber samples with varying qualities. RNA-seq technology was used to analyze the expression profiles of cotton fibers at the secondary cell wall (SCW) thickening stage (20, 25, and 30 days post-anthesis (DPA)). The results showed that a large number of differentially expressed genes (DEGs) were obtained from the three assessed cotton cultivars at different stages of SCW development. For instance, at 20 DPA, Sea Island cotton (HL) had 6,215 and 5,364 DEGs compared to upland cotton 17-24 (L) and 62-33 (S), respectively. Meanwhile, there were 1,236 DEGs between two upland cotton cultivars, 17-24 (L) and 62-33 (S). Gene Ontology (GO) term enrichment identified 42 functions, including 20 biological processes, 11 cellular components, and 11 molecular functions. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis identified several pathways involved in SCW synthesis and thickening, such as glycolysis/gluconeogenesis, galactose metabolism, propanoate metabolism, biosynthesis of unsaturated fatty acids pathway, valine, leucine and isoleucine degradation, fatty acid elongation pathways, and plant hormone signal transduction. Through the identification of shared DEGs, 46 DEGs were found to exhibit considerable expressional differences at different fiber stages from the three cotton cultivars. These shared DEGs have functions including REDOX enzymes, binding proteins, hydrolases (such as GDSL thioesterase), transferases, metalloproteins (cytochromatin-like genes), kinases, carbohydrates, and transcription factors (MYB and WRKY). Therefore, RT-qPCR was performed to verify the expression levels of nine of the 46 identified DEGs, an approach which demonstrated the reliability of RNA-seq data. Our results provided valuable molecular resources for clarifying the cell biology of SCW biosynthesis during fiber development in cotton.

Heterosis and combining ability for phenological yield and fiber traits of cotton (Gossypium hirsutum L.) genotypes

The seeds of 4 lines, 3 testers, and their 12 F1 hybrids were sown in a randomized complete block design (RCBD) with 3 replications at Botanical Garden, Department of Plant Breeding and Genetics, Sindh Agriculture University, Tandojam during Kharif 2019. F1 hybrids were raised for the estimation of heterotic effects, GCA and SCA for days to 1st squaring, days to 1st boll formation Bolls opened at 90 days after sowing, Sympodial branches plant-1, Bolls plant-1, Boll weight (g), Seed cotton yield plant-1 (g), 100-seed weight (g), Ginning outturn (%) and staple length (mm). Genotypes, parents, crosses, parent's v/s crosses, lines, testers and line × testers were significant for days to 1st squaring and days to 1st boll forming. Bolls unveiled their fissures precisely 90 days post-sowing, while parameters including sympodial branches per plant, bolls per plant, individual boll weight, seed cotton yield per plant, 100-seed weight, ginning outturn, and staple length underwent meticulous evaluation. The statistical scrutiny unveiled the insignificance of both lines and testers concerning the 90-day boll dehiscence. Similarly, the parental influence on boll weight, 100-seed weight, and staple length exhibited a lack of statistical significance. Line CRIS-134, Sindh, and tester FH-901 gave a higher mean performance for all the traits. Among the hybrids, Mehran × FH-901, Sindh-1 × CIM-602, CRIS-134 × CIM-602, CRIS-342 × Koonj, and CRIS-342 × CIM-602 gave a desirable mean performance and heterotic effect for all the traits. CRIS-342 × Koonj produced maximum SCA effects for bolls per plant. Mehran × FH-901 recorded higher SCA effects for seed cotton yield plant-1 and 100-seed weight, CRIS-342 × CIM-602 for lint percentage, and CRIS-342 × FH-901 for staple length. It is suggested that these lines and testers should be utilized in the breeding program to improve these traits.

Genetic analysis of yield and fiber quality traits in cotton (Gossypium hirsutum L.) under full and deficit irrigation conditions using full diallel method

The aim of the study was to assess the genetic structure and quantitative heritability of cotton yield, yield components and fiber quality parameters under well-watered (100%) and deficit (50%) irrigation conditions using a complete full diallel cross method with six cotton genotypes. The F1 and F2 generations were obtained to study the effect of irrigation conditions on genotypic variation and maternal effects on the traits studied. Parental, F1 and F2 generations were growed under full and deficit irrigation conditions and selected agronomic and fiber quality traits were measured. The data were analysed using various methods, including Griffing Method I, Model I analysis of variance, full diallel table analysis of variance, Jinks-Hayman diallel hybrid analysis. The Jinks-Hayman analysis of variance showed that dominant effects were more important in the inheritance of all traits, as indicated by the negative value of the difference between the additive variance and the dominance variance (D-H1). In addition, the average degree of dominance (H1/D)1/2 was greater than 1, indicating the predominance of dominant gene action in inheritance. The study concluded that starting selection in the F5–F6 generation is appropriate for drought resistant cotton breeding studies. It also emphasised the importance of conducting drought resistant cotton breeding under drought conditions due to the differences in gene movement between well-watered irrigation and drought stress conditions. The study highlighted the importance of population selection, environmental factors, data collection and analysis interpretation in breeding studies. It suggested that the Griffing diallel analysis method is suitable for hybrid breeding studies, while the Jinks-Hayman type analysis method is suitable for studying the genetic structures of populations.

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

Key messageA 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.