Genomic analyses reveal the genetic basis of early maturity and identification of loci and candidate genes in upland cotton (Gossypium hirsutum L.)

Genome-wide association study reveals significant loci and candidate genes for fruit branch length in upland cotton

The length of fruit branches significantly influences plant architecture in upland cotton (Gossypium hirsutum L.), which is crucial for optimizing fiber yield and quality. In this study, a comprehensive genome-wide association study was conducted based on whole-genome resequencing data that identified 249 significant SNPs associated with fruit branch length (FBL), forming 79 distinct quantitative trait loci (QTL) regions. Notably, stable QTL regions qFBL-A10-4 and qFBL-D03-17 were identified, harboring key candidate genes such as Ghir_A10G014390 and Ghir_D03G011390. Superior haplotypes of these genes significantly enhance FBL, fiber yield, and quality, offering valuable targets for cotton breeding programs focused on optimizing plant architecture and productivity.

Integrative GWAS and transcriptomics reveal GhAMT2 as a key regulator of cotton resistance to Verticillium wilt

Introduction

Verticillium wilt, incited by the soilborne fungus Verticillium dahliae, is a severe threat to global cotton (Gossypium spp.) production, resulting in significant yield losses and reduced fiber quality.

Methods

To uncover the genetic and molecular basis of resistance to this devastating disease, we combined genome-wide association study (GWAS) and transcriptomic analyses in a natural population of 355 upland cotton accessions.

Results

GWAS identified a stable major-effect quantitative trait locus (QTL), qVW-A01-2, on chromosome A01, which harbors the candidate gene GhAMT2, encoding a high-affinity ammonium transporter. Transcriptomic profiling revealed that GhAMT2 was significantly upregulated at 12 hours post-inoculation with V. dahliae, coinciding with the activation of immune signaling pathways. Weighted Gene Co-expression Network Analysis (WGCNA) further linked GhAMT2 to critical defense pathways, including lignin biosynthesis, salicylic acid signaling, and reactive oxygen species (ROS) homeostasis, suggesting its role in cell wall reinforcement and systemic immune responses. Functional validation through virus-induced gene silencing (VIGS) confirmed that silencing GhAMT2 compromised disease resistance. In contrast, transgenic Arabidopsis plants overexpressing GhAMT2 exhibited enhanced resistance to V. dahliae, demonstrating its essential role in defense regulation.

Discussion

These findings establish GhAMT2 as a key regulator of cotton resistance to Verticillium wilt and highlight its potential for marker-assisted breeding and genetic engineering to improve disease-resistant cotton varieties.

Comprehensive transcriptomic and metabolomic analysis revealed drought tolerance regulatory pathways in upland cotton

Cotton is a kind of cash crop widely planted in arid and semi-arid areas. In this study, we performed multi-omics analysis of two drought resistant extreme materials, Yumian 4 and C460, under drought stress. Transcriptome analysis showed that DY (post-drought stress Yumian 4) had more differentially expressed genes than DC (post-drought stress C460), and there were 10247 DEGs in the two comparison groups. Metabolomics analysis identified 1766 metabolites, which were divided into 12 classes. The up-regulated metabolites mainly included lipid accumulation, phenylpropanoid biosynthesis, and flavonoids. The combined transcriptome and metabolome analysis highlighted the importance of phenylpropanoid biosynthesis in enhancing drought tolerance. Combining the two omics analysis, it was found that the enrichment pathway of differential genes and differential metabolites is mainly in the phenylpropane biosynthesis pathway, which contains 23 related candidate genes. In summary, the results of multi-omics analysis of the two extreme drought resistance cotton materials showed that they enhanced drought resistance by affecting phenylpropanoid biosynthesis pathways. Promote the accumulation of osmotic substances. The results further deepen our understanding of the molecular mechanism of drought tolerance in cotton and provide new insights for molecular breeding of cotton.

The GhWRKY46-GhGAI Module Mediates Cotton Flowering by Regulating the Expression of Flowering Promotion Factors

Flowering represents a pivotal developmental transition stage in the life cycle of a plant, and the occurrence of flowering at the optimal time is critical for reproductive success. WRKY transcription factors play a vital role in a signaling network that governs a multitude of plant processes. Here, a gene, GhWRKY46, that was differentially expressed in early and late maturing materials was identified via association analysis, and it was specifically expressed in flower buds. Under natural light and temperature conditions, compared to Jin668, the flowering time of OE-GhWRKY46 plants was advanced by approximately 6 days, while the flowering time of CR-GhWRKY46 plants was delayed by approximately 8 days. Transcriptomic data indicated that overexpression or knockout of GhWRKY46 resulted in the activation or repression, respectively, of the photoperiod gene CO-Like and genes related to bud differentiation. Combined RNA-seq and DAP-seq analysis revealed that three genes, namely, GhCOL4, GhCOL2 and GhFPF1-like, may be expressed downstream of GhWRKY46. Dual-luciferase assays and electrophoretic mobility shift assays (EMSAs) demonstrated that GhWRKY46 could directly bind to the W-box and promote the expression of these genes. Similarly, GhFT was also found to be activated by GhWRKY46. Both in vivo and in vitro biochemical analyses demonstrated that GhWRKY46 interacted with GhGAI, and GhGAI could interfere with the transcriptional activation of GhWRKY46, which in turn inhibited the expression of GhCOL4, GhCOL2, GhFPF1-like, and GhFT. In conclusion, this study accurately predicted the GhWRKY46 binding motif, which is important for the construction of regulatory networks of the WRKY family in other crops and introduces a novel regulatory module for the flowering regulation pathway in cotton.

Identification and Expression Analysis of CCCH Zinc Finger Family Genes in Oryza sativa

BACKGROUND

CCCH zinc finger proteins (OsC3Hs) are a class of transcriptional regulators that play important roles in plant development and stress responses. Although their functional significance has been widely studied in model species, comprehensive genome-wide characterization of CCCH proteins in rice (Oryza sativa) remains limited.

METHODS

Using Arabidopsis CCCH proteins as references, we identified the CCCH gene family in rice and analyzed the physicochemical properties, subcellular localization, conserved structures, phylogeny, cis-regulatory elements, synteny analysis, spatiotemporal expression patterns, and expression patterns under drought, ABA, and MeJA treatments for the identified CCCH family members.

RESULTS

The results showed that the rice CCCH family comprises 73 members, which are unevenly distributed across the 12 chromosomes. Phylogenetic analysis classified them into 11 subfamilies. Subcellular localization indicated that most members are localized in the nucleus. The upstream regions of CCCH promoters contain a large number of cis-regulatory elements related to plant hormones and biotic stress responses. Most genes respond to drought, abscisic acid (ABA), and methyl jasmonate (MeJA) treatments. OsC3H36 was highly expressed under drought, ABA, and MeJA treatments. Haplotype analysis of this gene revealed two major allelic variants (H1 and H2), with H1 predominantly found in japonica rice and associated with increased grain width and 1000-grain weight. Functional validation using a chromosome segment substitution line (CSSL1) confirmed these findings.

CONCLUSIONS

CCCH genes play important roles in rice growth, development, and stress responses. Additionally, we validated that OsC3H36 is associated with rice grain width and 1000-grain weight.

A telomere-to-telomere genome assembly of cotton provides insights into centromere evolution and short-season adaptation

Cotton (Gossypium hirsutum L.) is a key allopolyploid crop with global economic importance. Here we present a telomere-to-telomere assembly of the elite variety Zhongmian 113. Leveraging technologies including PacBio HiFi, Oxford Nanopore Technology (ONT) ultralong-read sequencing and Hi-C, our assembly surpasses previous genomes in contiguity and completeness, resolving 26 centromeric and 52 telomeric regions, 5S rDNA clusters and nucleolar organizer regions. A phylogenetically recent centromere repositioning on chromosome D08 was discovered specific to G. hirsutum, involving deactivation of an ancestral centromere and the formation of a unique, satellite repeat-based centromere. Genomic analyses evaluated favorable allele aggregation for key agronomic traits and uncovered an early-maturing haplotype derived from an 11 Mb pericentric inversion that evolved early during G. hirsutum domestication. Our study sheds light on the genomic origins of short-season adaptation, potentially involving introgression of an inversion from primitively domesticated forms, followed by subsequent haplotype differentiation in modern breeding programs.

Characterization and functional analysis of CONSTANS-like 3 involved in photoperiodic flowering of Gossypium hirsutum

The CONSTANS-like (COL) family plays a pivotal role in regulating plant photoperiodic flowering pathways. Although several COLs have been characterized in Arabidopsis, their functions in cotton lack clarity. Here, GhCOL3, a gene of the COL family in cotton (Gossypium hirsutum), was cloned and characterized. GhCOL3 is located in the nucleus, and GhCOL3 was expressed in young leaves, hypocotyls, and flower organs and exhibited obvious circadian rhythms under long-day conditions. Overexpressing of GhCOL3 heterogeneously in Arabidopsis thaliana led to delayed flowering, whereas silencing of GhCOL3 in cotton using the virus-induced gene silencing system led to earlier flowering, suggesting a negative regulatory role of GhCOL3 in plant flowering. Transcriptome analysis and expression detection showed that bHLH38, bHLH100, bHLH101, and BBX31 were significantly upregulated in GhCOL3 heterogeneous overexpression lines, whereas the expression of FT was downregulated. Moreover, the expression of GhbHLH38, GhBBX31, and GhFT were significantly affected in the GhCOL3-silenced line, thus laying the foundation for elucidating the regulatory mechanism of GhCOL3 in cotton flowering.

QTL Mapping and Candidate Gene Analysis for Cotton Fiber Quality and Early Maturity Using F2 and F3 Generations

Cotton is the most important natural fiber-producing crop globally. High-quality fiber and early maturity are equally important breeding goals in the cotton industry. However, it remains challenging to synchronously improve these traits through conventional breeding techniques. To identify additional genetic information relating to fiber quality and early maturity, 11 phenotypic traits for the F2 and F3 generations were tested, and quantitative trait loci (QTL) mapping was performed. Candidate genes were analyzed using published RNA-seq datasets and qRT-PCR assays. All 11 tested traits showed bi-directional transgressive segregation, and most traits followed an approximately normal distribution. Overall, significant positive and significant negative correlations were observed among these traits. During cotton breeding, varieties with strong boll-setting ability can be selected from early-maturing materials that have high-quality fiber. A total of 102 QTLs were mapped, including 4 major and 3 stable QTLs. qFL-D13-1 was mapped in both the F2 and F3 generations, achieving a 3.94% to 11.39% contribution rate to the phenotypic variation. Three genes located in the QTL regions were identified based on their high expression levels in the three evaluated RNA-seq datasets. Ghir_A04G014830.1, covered by qHNFFB-A4-1 and qFU-A4-1, encoded ACLA-1. Ghir_D13G015010.1, encoding VTC2, and Ghir_D13G016670.1, encoding GA2OX1, were in the stable QTL qFL-D13-1 region. The qRT-PCR results suggested that these three genes may be involved in regulating seed development, fiber initiation, and fiber elongation. Overall, these findings contribute additional information for the breeding of high-yield, high fiber quality, and early-maturity varieties, as well as serve as a foundation for research on the underlying molecular mechanisms.

Identification of Elite Alleles and Candidate Genes for the Cotton Boll Opening Rate via a Genome-Wide Association Study

The boll opening rate (BOR) is an early maturity trait that plays a crucial role in cotton production in China, as BOR has a significant effect on defoliant spraying and picking time of unginned cotton, ultimately determining yield and fiber quality. Therefore, elucidating the genetic basis of BOR and identifying stably associated loci, elite alleles, and potential candidate genes can effectively accelerate the molecular breeding process. In this study, we utilized the mixed linear model (MLM) algorithm to perform a genome-wide association study (GWAS) based on 4,452,629 single-nucleotide polymorphisms (SNPs) obtained through whole-genome resequencing of a natural population of 418 upland cotton accessions and phenotypic BOR data acquired from five environments. A total of 18 SNP loci were identified on chromosome D11 that are stable and significantly associated with BOR in multiple environments. Moreover, a significant SNP peak (23.703-23.826 Mb) was identified, and a GH-D11G2034 gene and favorable allelic variation (GG) related to BOR were found in this genomic region, significantly increasing cotton BOR. Evolutionary studies have shown that GH-D11G2034 may have been subjected to artificial selection throughout the variety selection process. This study provides valuable insights and suggests that the GH-D11G2034 gene and its favorable allelic variation (GG) could be potential targets for molecular breeding to improve BOR in upland cotton. However, further research is needed to validate the function of this gene and explore its potential applications in cotton breeding programs. Overall, this study contributes to the advancement of genetic improvement in early maturity and has important implications for the sustainable development of the cotton industry.

Exploring Metabolic Pathways and Gene Mining During Cotton Flower Bud Differentiation Stages Based on Transcriptomics and Metabolomics

Cotton is regarded as one of the significant economic crops in China, and its earliness is defined as one of the crucial traits influencing fiber quality and yield. To study the physiological and biochemical mechanisms related to early-maturing traits of cotton, cotton shoot apexes at the one-leaf, three-leaf, and five-leaf stages of the early-maturing cotton CCRI50 and late-maturing cotton Guoxinmian11 were collected for transcriptome sequencing and metabolomics, respectively. A total of 616, 782, and 842 differentially expressed genes (DEGs) at the one-leaf stage, three-leaf stage, and five-leaf stage were obtained through transcriptome sequencing, respectively. The metabolic detection results showed that 68, 56, and 62 differential metabolites (DMs) were obtained in the three periods, respectively. A total of 10 DMs were detected simultaneously from the one-leaf to five-leaf stage, 4 of which were phenolic acids and down-regulated in the early maturing variety CCRI50. A combined transcriptomic and metabolomic analysis revealed that phenylpropanoid biosynthesis, tyrosine metabolism, and phenylalanine metabolism might be important metabolic pathways in cotton bud differentiation. GhTYDC-A01 was identified in both the tyrosine metabolism and phenylalanine metabolism pathways, and it was highly expressed in pistils. To investigate the function of this gene in flowering, we overexpressed it in Arabidopsis thaliana. Compared to the wild type, the flowering time of the overexpression of GhTYDC-A01 in Arabidopsis was delayed. This study provides valuable resources and new insights into the relationship between metabolites and early-maturing cotton.

Identification of QTLs for early maturity-related traits based on RIL population of two elite cotton cultivars

BACKGROUND

Early-maturity cotton varieties have the potential to be cultivated in a wider geographical area, extending as far north as 46 °N in China, and confer to address the issue of competition for land between grain and cotton by reducing their whole growth period (WGP). Therefore, it is of great importance to develop cotton varieties with comprehensive early maturity and high yield following investigating the regulatory mechanism underlying early maturity and identifying early maturity-related genes.

RESULTS

In this study, 'SCRC19' and 'SCRC21', two excellent cultivars with significantly different WGP, along with their recombinant inbred lines (RILs) consisting of 150 individuals were re-sequenced, yielding 4,092,677 high-quality single nucleotide polymorphisms (SNPs) and 794 bin markers across 26 chromosomes. A genetic map spanning 2213.71 cM was constructed using the 794 bin markers. Based on this map, we identified a total of 78 early maturity-related QTLs, including 12 QTLs for WGP, 4 for SSP, 12 for SFP, 3 for FBP, 11 for NFFB, 8 for NFB, 16 for HNFFB and 12 for PH. Six QTL clusters, each containing more than four traits, were identified. One particular QTL cluster, which had the largest number of QTLs, ranged from 108.5 cM to 109 cM on Dt3, and contained 39 genes. Through functional analysis, we highlighted two early maturity-related candidates of GH_D03G1554 and GH_D03G1541, which were annotated as a BEL1-like homeodomain protein 8 and a homeobox-leucine zipper family protein, respectively.

CONCLUSIONS

We have identified a QTL cluster related to six early maturity-associated traits on Dt3. Through annotation of genes from candidate region, we have identified two candidate genes, GH_D03G1554 and GH_D03G1541, whose expression levels in 'SCRC21' were significantly higher than those in 'SCRC19' at different stages of flower bud development. These candidate genes provide new insights into the study of early-maturity mechanism and offer potential genetic improvement of cotton.

Fashion meets science: how advanced breeding approaches could revolutionize the textile industry

Natural fibers have garnered considerable attention owing to their desirable textile properties and advantageous effects on human health. Nevertheless, natural fibers lag behind synthetic fibers in terms of both quality and yield, as these attributes are largely genetically determined. In this article, a comprehensive overview of the natural and synthetic fiber production landscape over the last 10 years is presented, with a particular focus on the role of scientific breeding techniques in improving fiber quality traits in key crops like cotton, hemp, ramie, and flax. Additionally, the article delves into cutting-edge genomics-assisted breeding techniques, including QTL mapping, genome-wide association studies, transgenesis, and genome editing, and their potential role in enhancing fiber quality traits in these crops. A user-friendly compendium of 11226 available QTLs and significant marker-trait associations derived from 136 studies, associated with diverse fiber quality traits in these crops is furnished. Furthermore, the potential applications of transcriptomics in these pivotal crops, elucidating the distinct genes implicated in augmenting fiber quality attributes are investigated. Additionally, information on 11257 candidate/characterized or cloned genes sourced from various studies, emphasizing their key role in the development of high-quality fiber crops is collated. Additionally, the review sheds light on the current progress of marker-assisted selection for fiber quality traits in each crop, providing detailed insights into improved cultivars released for different fiber crops. In conclusion, it is asserted that the application of modern breeding tools holds tremendous potential in catalyzing a transformative shift in the textile industry.

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.

Leveraging transcriptomics-based approaches to enhance genomic prediction: integrating SNPs and gene networks for cotton fibre quality improvement

Cultivated cotton plants are the world's largest source of natural fibre, where yield and quality are key traits for this renewable and biodegradable commodity. The Gossypium hirsutum cotton genome contains ~80K protein-coding genes, making precision breeding of complex traits a challenge. This study tested approaches to improving the genomic prediction (GP) accuracy of valuable cotton fibre traits to help accelerate precision breeding. With a biology-informed basis, a novel approach was tested for improving GP for key cotton fibre traits with transcriptomics of key time points during fibre development, namely, fibre cells undergoing primary, transition, and secondary wall development. Three test approaches included weighting of SNPs in DE genes overall, in target DE gene lists informed by gene annotation, and in a novel approach of gene co-expression network (GCN) clusters created with partial correlation and information theory (PCIT) as the prior information in GP models. The GCN clusters were nucleated with known genes for fibre biomechanics, i.e., fasciclin-like arabinogalactan proteins, and cluster size effects were evaluated. The most promising improvements in GP accuracy were achieved by using GCN clusters for cotton fibre elongation by 4.6%, and strength by 4.7%, where cluster sizes of two and three neighbours proved most effective. Furthermore, the improvements in GP were due to only a small number of SNPs, in the order of 30 per trait using the GCN cluster approach. Non-trait-specific biological time points, and genes, were found to have neutral effects, or even reduced GP accuracy for certain traits. As the GCN clusters were generated based on known genes for fibre biomechanics, additional candidate genes were identified for fibre elongation and strength. These results demonstrate that GCN clusters make a specific and unique contribution in improving the GP of cotton fibre traits. The findings also indicate that there is room for incorporating biology-based GCNs into GP models of genomic selection pipelines for cotton breeding to help improve precision breeding of target traits. The PCIT-GCN cluster approach may also hold potential application in other crops and trees for enhancing breeding of complex traits.

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

KEY MESSAGE

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 (A05:14.64-15.64 Mb) 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.

Genome-Wide Identification and Bioinformatics Analysis of the FK506 Binding Protein Family in Rice

The FK506 Binding Protein (FKBP), ubiquitously present across diverse species, is characterized by its evolutionarily conserved FK506 binding domain (FKBd). In plants, evidence suggests that this gene family plays integral roles in regulating growth, development, and responses to environmental stresses. Notably, research on the identification and functionality of FKBP genes in rice remains limited. Therefore, this study utilized bioinformatic tools to identify 30 FKBP-encoding genes in rice. It provides a detailed analysis of their chromosomal locations, evolutionary relationships with the Arabidopsis thaliana FKBP family, and gene structures. Further analysis of the promoter elements of these rice FKBP genes revealed a high presence of stress-responsive elements. Quantitative PCR assays under drought and heat stress conditions demonstrated that genes OsFKBP15-2, OsFKBP15-3, OsFKBP16-3, OsFKBP18, and OsFKBP42b are inducible by these adverse conditions. These findings suggest a significant role for the rice FKBP gene family in stress adaptation. This research establishes a critical foundation for deeper explorations of the functional roles of the OsFKBP genes in rice.

Genome-wide identification and mining elite allele variation of the Monoacylglycerol lipase (MAGL) gene family in upland cotton (Gossypium hirsutum L.)

BACKGROUND

Monoacylglycerol lipase (MAGL) genes belong to the alpha/beta hydrolase superfamily, catalyze the terminal step of triglyceride (TAG) hydrolysis, converting monoacylglycerol (MAG) into free fatty acids and glycerol.

RESULTS

In this study, 30 MAGL genes in upland cotton have been identified, which have been classified into eight subgroups. The duplication of GhMAGL genes in upland cotton was predominantly influenced by segmental duplication events, as revealed through synteny analysis. Furthermore, all GhMAGL genes were found to contain light-responsive elements. Through comprehensive association and haplotype analyses using resequencing data from 355 cotton accessions, GhMAGL3 and GhMAGL6 were detected as key genes related to lipid hydrolysis processes, suggesting a negative regulatory effect.

CONCLUSIONS

In summary, MAGL has never been studied in upland cotton previously. This study provides the genetic mechanism foundation for the discover of new genes involved in lipid metabolism to improve cottonseed oil content, which will provide a strategic avenue for marker-assisted breeding aimed at incorporating desirable traits into cultivated cotton varieties.

Multistage temporal transcriptomic atlas unveils major contributor to reproductive phase in upland cotton

Flowering is a major developmental transition in plants, but asynchronous flowering hinders the utilization of wild cotton relatives in breeding programs. We performed comparative transcriptomic profiling of early- and late-flowering Gossypium hirsutum genotypes to elucidate genetic factors influencing reproductive timing. Shoot apices were sampled from the photoperiod-sensitive landrace G. hirsutum purpurascens (GhP) and early-maturing variety ZhongMianSuo (ZMS) at five time points following the emergence of sympodial nodes. RNA-sequencing revealed extensive transcriptional differences during floral transition. Numerous flowering-associated genes exhibited genotype-specific expression, including FLOWERING LOCUS T (FT) homologs upregulated in ZMS. FT-interacting factors like SOC1 and CO-like also showed higher expression in ZMS, implicating florigen pathways in early flowering. Additionally, circadian clock and light signalling components were misregulated between varieties, suggesting altered photoperiod responses in GhP. Weighted co-expression network analysis specifically linked a module enriched for circadian-related genes to GhP's late flowering. Through an integrated transcriptome analysis, we defined a regulatory landscape of reproductive phase change in cotton. Differentially expressed genes related to photoperiod, circadian clock, and light signalling likely contribute to delayed flowering in wild cottons. Characterization of upstream flowering regulators will enable modifying photoperiod sensitivity and expand germplasm use for cotton improvement. This study provides candidate targets for elucidating interactive mechanisms that control cotton flowering time across diverse genotypes.

Identification and characterization of ACR gene family in maize for salt stress tolerance

Background

Members of the ACR gene family are commonly involved in various physiological processes, including amino acid metabolism and stress responses. In recent decades, significant progress has been made in the study of ACR genes in plants. However, little is known about their characteristics and function in maize.

Methods

In this study, ACR genes were identified from the maize genome, and their molecular characteristics, gene structure, gene evolution, gene collinearity analysis, cis-acting elements were analyzed. qRT-PCR technology was used to verify the expression patterns of the ZmACR gene family in different tissues under salt stress. In addition, Ectopic expression technique of ZmACR5 in Arabidopsis thaliana was utilized to identify its role in response to salt stress.

Results

A total of 28 ZmACR genes were identified, and their molecular characteristics were extensively described. Two gene pairs arising from segmented replication events were detected in maize, and 18 collinear gene pairs were detected between maize and 3 other species. Through phylogenetic analysis, three subgroups were revealed, demonstrating distinct divergence between monocotyledonous and dicotyledonous plants. Analysis of ZmACR cis-acting elements revealed the optional involvement of ZmACR genes in light response, hormone response and stress resistance. Expression analysis of 8 ZmACR genes under salt treatment clearly revealed their role in the response to salt stress. Ectopic overexpression of ZmACR5 in Arabidopsis notably reduced salt tolerance compared to that of the wild type under salt treatment, suggesting that ZmACR5 has a negative role in the response to salt stress.

Conclusion

Taken together, these findings confirmed the involvement of ZmACR genes in regulating salt stress and contributed significantly to our understanding of the molecular function of ACR genes in maize, facilitating further research in this field.

Selective sweep and GWAS provide insights into adaptive variation of Populus cathayana leaves

Leaf morphology plays a crucial role in predicting the productivity and environmental adaptability of forest trees, making it essential to understand the genetic mechanisms behind leaf variation. In natural populations of Populus cathayana, leaf morphology exhibits rich intraspecific variation due to long-term selection. However, there have been no studies that systematically reveal the genetic mechanisms of leaf variation in P. cathayana. To fill this gap and enhance our understanding of leaf variation in P. cathayana, we collected nine leaf traits from the P. cathayana natural population, consisting of 416 accessions, and conducted the preliminary classification of leaf types with four categories. Subsequently, we conducted an analysis of selective sweep and genome-wide association studies (GWAS) to uncover the genetic basis of leaf traits variation. Most of the leaf traits displayed significant correlations, with broad-sense trait heritability ranging from 0.38 to 0.74. In total, three selective sweep methods ultimately identified 278 positively selected candidate regions and 493 genes associated with leaf size. Single-trait and multi-trait GWAS methods detected 13 and 59 genes, respectively. By integrating the results of selective sweep and GWAS, we further identified a total of nine overlapping genes. These genes may play a role in the leaf development process and are closely associated with leaf size. In particular, the gene CBSCBSPB3 (Pca07G009100) located on chromosome 7, was associated with the response to light stimulation. This study will deepen our understanding of the genetic mechanism of leaf adaptive variation in P. cathayana and provide valuable gene resources.

Genomic loci associated with leaf abscission contribute to machine picking and environmental adaptability in upland cotton (Gossypium hirsutum L.)

INTRODUCTION

Defoliation by applying defoliants before machine picking is an important agricultural practice that enhances harvesting efficiency and leads to increased raw cotton purity. However, the fundamental characteristics of leaf abscission and the underlying genetic basis in cotton are not clearly understood.

OBJECTIVES

In this study, we aimed to (1) reveal the phenotypic variations in cotton leaf abscission, (2) discover the whole-genome differentiation sweeps and genetic loci related to defoliation, (3) identify and verify the functions of key candidate genes associated with defoliation, and (4) explore the relationship between haplotype frequency of loci and environmental adaptability.

METHODS

Four defoliation-related traits of 383 re-sequenced Gossypium hirsutum accessions were investigated in four environments. The genome-wide association study (GWAS), linkage disequilibrium (LD) interval genotyping and functional identification were conducted. Finally, the haplotype variation related to environmental adaptability and defoliation traits was revealed.

RESULTS

Our findings revealed the fundamental phenotypic variations of defoliation traits in cotton. We showed that defoliant significantly increased the defoliation rate without incurring yield and fiber quality penalties. The strong correlations between defoliation traits and growth period traits were observed. A genome-wide association study of defoliation traits identified 174 significant SNPs. Two loci (RDR7 on A02 and RDR13 on A13) that significantly associated with the relative defoliation rate were described, and key candidate genes GhLRR and GhCYCD3;1, encoding a leucine-rich repeat (LRR) family protein and D3-type cell cyclin 1 protein respectively, were functional verified by expression pattern analysis and gene silencing. We found that combining of two favorable haplotypes (HapRDR7 and HapRDR13) improved sensitivity to defoliant. The favorable haplotype frequency generally increased in high latitudes in China, enabling adaptation to the local environment.

CONCLUSION

Our findings lay an important foundation for the potentially broad application of leveraging key genetic loci in breeding machine-pickable cotton.

Genetic interrogation of phenotypic plasticity informs genome-enabled breeding in cotton

Phenotypic plasticity, or the ability to adapt to and thrive in changing climates and variable environments, is essential for developmental programs in plants. Despite its importance, the genetic underpinnings of phenotypic plasticity for key agronomic traits remain poorly understood in many crops. In this study, we aim to fill this gap by using genome-wide association studies to identify genetic variations associated with phenotypic plasticity in upland cotton (Gossypium hirsutum L.). We identified 73 additive quantitative trait loci (QTLs), 32 dominant QTLs, and 6799 epistatic QTLs associated with 20 traits. We also identified 117 additive QTLs, 28 dominant QTLs, and 4691 epistatic QTLs associated with phenotypic plasticity in 19 traits. Our findings reveal new genetic factors, including additive, dominant, and epistatic QTLs, that are linked to phenotypic plasticity and agronomic traits. Meanwhile, we find that the genetic factors controlling the mean phenotype and phenotypic plasticity are largely independent in upland cotton, indicating the potential for simultaneous improvement. Additionally, we envision a genomic design strategy by utilizing the identified QTLs to facilitate cotton breeding. Taken together, our study provides new insights into the genetic basis of phenotypic plasticity in cotton, which should be valuable for future breeding.

Synergistic optimization of crops by combining early maturation with other agronomic traits

Many newly created early maturing varieties exhibit poor stress resistance and low yield, whereas stress-resistant varieties are typically late maturing. For this reason, the polymerization of early maturity and other desired agronomic qualities requires overcoming the negative connection between early maturity, multi-resistance, and yield, which presents a formidable challenge in current breeding techniques. We review the most salient constraints of early maturity breeding in current crop planting practices and the molecular mechanisms of different maturation timeframes in diverse crops from their origin center to production areas. We explore current breeding tactics and the future direction of crop breeding and the issues that must be resolved to accomplish the polymerization of desirable traits in light of the current obstacles and limitations.

A comprehensive overview of cotton genomics, biotechnology and molecular biological studies

Cotton is an irreplaceable economic crop currently domesticated in the human world for its extremely elongated fiber cells specialized in seed epidermis, which makes it of high research and application value. To date, numerous research on cotton has navigated various aspects, from multi-genome assembly, genome editing, mechanism of fiber development, metabolite biosynthesis, and analysis to genetic breeding. Genomic and 3D genomic studies reveal the origin of cotton species and the spatiotemporal asymmetric chromatin structure in fibers. Mature multiple genome editing systems, such as CRISPR/Cas9, Cas12 (Cpf1) and cytidine base editing (CBE), have been widely used in the study of candidate genes affecting fiber development. Based on this, the cotton fiber cell development network has been preliminarily drawn. Among them, the MYB-bHLH-WDR (MBW) transcription factor complex and IAA and BR signaling pathway regulate the initiation; various plant hormones, including ethylene, mediated regulatory network and membrane protein overlap fine-regulate elongation. Multistage transcription factors targeting CesA 4, 7, and 8 specifically dominate the whole process of secondary cell wall thickening. And fluorescently labeled cytoskeletal proteins can observe real-time dynamic changes in fiber development. Furthermore, research on the synthesis of cotton secondary metabolite gossypol, resistance to diseases and insect pests, plant architecture regulation, and seed oil utilization are all conducive to finding more high-quality breeding-related genes and subsequently facilitating the cultivation of better cotton varieties. This review summarizes the paramount research achievements in cotton molecular biology over the last few decades from the above aspects, thereby enabling us to conduct a status review on the current studies of cotton and provide strong theoretical support for the future direction.

Identification of novel candidate loci and genes for seed vigor-related traits in upland cotton (Gossypium hirsutum L.) via GWAS

Seed vigor (SV) is a crucial trait determining the quality of crop seeds. Currently, over 80% of China's cotton-planting area is in Xinjiang Province, where a fully mechanized planting model is adopted, accounting for more than 90% of the total fiber production. Therefore, identifying SV-related loci and genes is crucial for improving cotton yield in Xinjiang. In this study, three seed vigor-related traits, including germination potential, germination rate, and germination index, were investigated across three environments in a panel of 355 diverse accessions based on 2,261,854 high-quality single-nucleotide polymorphisms (SNPs). A total of 26 significant SNPs were detected and divided into six quantitative trait locus regions, including 121 predicted candidate genes. By combining gene expression, gene annotation, and haplotype analysis, two novel candidate genes (Ghir_A09G002730 and Ghir_D03G009280) within qGR-A09-1 and qGI/GP/GR-D03-3 were associated with vigor-related traits, and Ghir_A09G002730 was found to be involved in artificial selection during cotton breeding by population genetic analysis. Thus, understanding the genetic mechanisms underlying seed vigor-related traits in cotton could help increase the efficiency of direct seeding by molecular marker-assisted selection breeding.

Genome-wide identification of R-SNARE gene family in upland cotton and function analysis of GhVAMP72l response to drought stress

Soluble N-ethylmaleimide-sensitive factor attachment protein receptors (R-SNAREs) mainly promoted the assembly of the SNARE complex to drive the final membrane fusion step of membrane transport. Previous research on R-SNAREs has mainly focused on development and growth and has rarely been involved in abiotic stress, especially in cotton. Here, we performed a comprehensive analysis of R-SNARE genes in upland cotton. In total, 51 Gh-R-SNARE genes across six phylogenetic groups were unevenly distributed on 21 chromosomes. Cis elements related to plant growth and response to abiotic stress responses were found in the promoter region of Gh-R-SNAREs. Nine Gh-R-SNARE genes were obviously upregulated under drought stress conditions by RNA-seq and qRT-PCR analysis. Among them, GhVAMP72l might be the key candidate gene contributing to drought stress tolerance in cotton by virus-induced gene silencing (VIGS) assay. These results provide valuable insights for the functional analysis of cotton R-SNAREs in response to drought stress and highlight potential beneficial genes for genetic improvement and breeding in cotton.

GhAP1-D3 positively regulates flowering time and early maturity with no yield and fiber quality penalties in upland cotton

Flowering time (FTi) is a major factor determining how quickly cotton plants reach maturity. Early maturity greatly affects lint yield and fiber quality and is crucial for mechanical harvesting of cotton in northwestern China. Yet, few quantitative trait loci (QTLs) or genes regulating early maturity have been reported in cotton, and the underlying regulatory mechanisms are largely unknown. In this study, we characterized 152, 68, and 101 loci that were significantly associated with the three key early maturity traits-FTi, flower and boll period (FBP) and whole growth period (WGP), respectively, via four genome-wide association study methods in upland cotton (Gossypium hirsutum). We focused on one major early maturity-related genomic region containing three single nucleotide polymorphisms on chromosome D03, and determined that GhAP1-D3, a gene homologous to Arabidopsis thaliana APETALA1 (AP1), is the causal locus in this region. Transgenic plants overexpressing GhAP1-D3 showed significantly early flowering and early maturity without penalties for yield and fiber quality compared to wild-type (WT) plants. By contrast, the mutant lines of GhAP1-D3 generated by genome editing displayed markedly later flowering than the WT. GhAP1-D3 interacted with GhSOC1 (SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1), a pivotal regulator of FTi, both in vitro and in vivo. Changes in GhAP1-D3 transcript levels clearly affected the expression of multiple key flowering regulatory genes. Additionally, DNA hypomethylation and high levels of H3K9ac affected strong expression of GhAP1-D3 in early-maturing cotton cultivars. We propose that epigenetic modifications modulate GhAP1-D3 expression to positively regulate FTi in cotton through interaction of the encoded GhAP1 with GhSOC1 and affecting the transcription of multiple flowering-related genes. These findings may also lay a foundation for breeding early-maturing cotton varieties in the future.

First Report on the Genetic Diversity of Populations of Gossypium barbadense L. and Gossypium hirsutun L. in the Amazonian Native Communities, Cusco-Peru

The genus Gossypium has important ethnobotanical and economic value for Amazonian Native Communities (A.N.C.). However, little research has been undertaken on the distribution and genetic diversity of cotton populations maintained in the Peruvian rainforest. This work aims to present the first report on the genetic diversity of Gossypium spp. populations in the A.N.C. of the province of La Convención, Cusco-Peru. The methodology was based on exploring, collecting, identifying, and characterizing the Gossypium populations present in the A.N.C. Twenty-six descriptors were evaluated (9 quantitative and 17 qualitative), and with this information, distribution, correlation, and principal component (PC) analyses were carried out. As a result, plants of two species [G. barbadense L. (44 samples) and G. hirsutum L. (19 samples)], one variety [G. barbadense var. brasiliensis (75 samples)], and three previously unidentified variations (9 samples) were identified. Altogether, 147 samples were collected. G. barbadense var. brasiliensis, which was always found in association with other economic crops within an altitude range of 338 to 1086 m, was the most predominant (51%), distributed in eleven A.N.C. and always in small plots (up to 2 ha). G. barbadense L. was cultivated between 397 and 1137 m of altitude in eight A.N.C. in plots of up to 3 ha in marginal lands. G. hirsutum L., with a smaller distribution (13%), was found between 334 and 497 m of altitude in only three communities; this species is cultivated in marginal areas throughout the year. The variability found for the first two PCs when considering the quantitative and qualitative descriptors was high (74.7%) and moderate (48.2%), respectively. When combining all the descriptors, the analysis showed that the first two PCs accounted for 51.8% of the total variability of the data. The PCs of the two types of data and their combination confirmed that the three populations found were grouped. The nine undefined samples were close to or intermediate between the described ones, showing that these samples may be the result of spontaneous crosses; as such, these samples need to be better evaluated with other tools for further definition. The information obtained shows that in the A.N.C. of Cusco-Peru, there is variability conserved by the inhabitants, who have been able to maintain and use these genotypes, even from their Amazonian indigenous ancestry, and the environment has been able to generate variability among the species, as will be highlighted in future works.

Dissection of the Pearl of Csaba pedigree identifies key genomic segments related to early ripening in grape

Pearl of Csaba (PC) is a valuable backbone parent for early-ripening grapevine (Vitis vinifera) breeding, from which many excellent early ripening varieties have been bred. However, the genetic basis of the stable inheritance of its early ripening trait remains largely unknown. Here, the pedigree, consisting of 40 varieties derived from PC, was re-sequenced for an average depth of ∼30×. Combined with the resequencing data of 24 other late-ripening varieties, 5,795,881 high-quality single nucleotide polymorphisms (SNPs) were identified following a strict filtering pipeline. The population genetic analysis showed that these varieties could be distinguished clearly, and the pedigree was characterized by lower nucleotide diversity and stronger linkage disequilibrium than the non-pedigree varieties. The conserved haplotypes (CHs) transmitted in the pedigree were obtained via identity-by-descent analysis. Subsequently, the key genomic segments were identified based on the combination analysis of haplotypes, selective signatures, known ripening-related quantitative trait loci (QTLs), and transcriptomic data. The results demonstrated that varieties with a superior haplotype, H1, significantly (one-way ANOVA, P < 0.001) exhibited early grapevine berry development. Further analyses indicated that H1 encompassed VIT_16s0039g00720 encoding a folate/biopterin transporter protein (VvFBT) with a missense mutation. VvFBT was specifically and highly expressed during grapevine berry development, particularly at veraison. Exogenous folate treatment advanced the veraison of "Kyoho". This work uncovered core haplotypes and genomic segments related to the early ripening trait of PC and provided an important reference for the molecular breeding of early-ripening grapevine varieties.

Recent advances and future perspectives in early-maturing cotton research

Cotton's fundamental requirements for long periods of growth and specific seasonal temperatures limit the global arable areas that can be utilized to cultivate cotton. This constraint can be alleviated by breeding for early-maturing varieties. By delaying the sowing dates without impacting the boll-opening time, early-maturing varieties not only mitigate the yield losses brought on by unfavorable weathers in early spring and late autumn but also help reducing the competition between cotton and other crops for arable land, thereby optimizing the cropping system. This review presents studies and breeding efforts for early-maturing cotton, which efficiently pyramid early maturity, high-quality, multiresistance traits, and suitable plant architecture by leveraging pleiotropic genes. Attempts are also made to summarize our current understanding of the molecular mechanisms underlying early maturation, which involves many pathways such as epigenetic, circadian clock, and hormone signaling pathways. Moreover, new avenues and effective measures are proposed for fine-scale breeding of early-maturing crops to ensure the healthy development of the agricultural industry.

Recent progression and future perspectives in cotton genomic breeding

Upland cotton is an important global cash crop for its long seed fibers and high edible oil and protein content. Progress in cotton genomics promotes the advancement of cotton genetics, evolutionary studies, functional genetics, and breeding, and has ushered cotton research and breeding into a new era. Here, we summarize high-impact genomics studies for cotton from the last 10 years. The diploid Gossypium arboreum and allotetraploid Gossypium hirsutum are the main focus of most genetic and genomic studies. We next review recent progress in cotton molecular biology and genetics, which builds on cotton genome sequencing efforts, population studies, and functional genomics, to provide insights into the mechanisms shaping abiotic and biotic stress tolerance, plant architecture, seed oil content, and fiber development. We also suggest the application of novel technologies and strategies to facilitate genome-based crop breeding. Explosive growth in the amount of novel genomic data, identified genes, gene modules, and pathways is now enabling researchers to utilize multidisciplinary genomics-enabled breeding strategies to cultivate "super cotton", synergistically improving multiple traits. These strategies must rise to meet urgent demands for a sustainable cotton industry.

QTL mapping and BSA-seq map a major QTL for the node of the first fruiting branch in cotton

Understanding the genetic basis of the node of the first fruiting branch (NFFB) improves early-maturity cotton breeding. Here we report QTL mapping on 200 F2 plants and derivative F2:3 and F2:4 populations by genotyping by sequencing (GBS). BC1F2 population was constructed by backcrossing one F2:4 line with the maternal parent JF914 and used for BSA-seq for further QTL mapping. A total of 1,305,642 SNPs were developed between the parents by GBS, and 2,907,790 SNPs were detected by BSA-seq. A high-density genetic map was constructed containing 11,488 SNPs and spanning 4,202.12 cM in length. A total of 13 QTL were mapped in the 3 tested populations. JF914 conferred favorable alleles for 11 QTL, and JF173 conferred favorable alleles for the other 2 QTL. Two stable QTL were repeatedly mapped in F2:3 and F2:4, including qNFFB-D3-1 and qNFFB-D6-1. Only qNFFB-D3-1 contributed more than 10% of the phenotypic variation. This QTL covered about 24.7 Mb (17,130,008-41,839,226 bp) on chromosome D3. Two regions on D3 (41,779,195-41,836,120 bp, 41,836,768-41,872,287 bp) were found by BSA-seq and covered about 92.4 Kb. This 92.4 Kb region overlapped with the stable QTL qNFFB-D3-1 and contained 8 annotated genes. By qRT-PCR, Ghir_D03G012430 showed a lower expression level from the 1- to 2-leaf stage and a higher expression level from the 3- to 6-leaf stage in the buds of JF173 than that of JF914. Ghir_D03G012390 reached the highest level at the 3- and 5-leaf stages in the buds of JF173 and JF914, respectively. As JF173 has lower NFFB and more early maturity than JF914, these two genes might be important in cell division and differentiation during NFFB formation in the seedling stage. The results of this study will facilitate a better understanding of the genetic basis of NFFB and benefit cotton molecular breeding for improving earliness traits.

SEP-like genes of Gossypium hirsutum promote flowering via targeting different loci in a concentration-dependent manner

SEP genes are famous for their function in the morphological novelty of bisexual flowers. Although the diverse functions of SEP genes were reported, only the regulatory mechanisms underlying floral organ development have been addressed. In this study, we identified SEP-like genes in Gossypium and found that SEP3 genes were duplicated in diploid cotton varieties. GhSEP4.1 and GhSEP4.2 were abundantly transcribed in the shoot apical meristem (SAM), but only GhSEP4.2 was expressed in the leaf vasculature. The expression pattern of GhSEPs in floral organs was conserved with that of homologs in Arabidopsis, except for GhSEP2 that was preponderantly expressed in ovules and fibers. The overexpression and silencing of each single GhSEP gene suggested their distinct role in promoting flowering via direct binding to GhAP1 and GhLFY genomic regions. The curly leaf and floral defects in overexpression lines with a higher expression of GhSEP genes revealed the concentration-dependent target gene regulation of GhSEP proteins. Moreover, GhSEP proteins were able to dimerize and interact with flowering time regulators. Together, our results suggest the dominant role of GhSEP4.2 in leaves to promote flowering via GhAP1-A04, and differently accumulated GhSEP proteins in the SAM alternately participate in forming the dynamic tetramer complexes to target at the different loci of GhAP1 and GhLFY to maintain reproductive growth. The regulatory roles of cotton SEP genes reveal their conserved and diversified functions.

GhCDPK60 positively regulates drought stress tolerance in both transgenic Arabidopsis and cotton by regulating proline content and ROS level

Calcium-Dependent Protein Kinases (CDPKs) involved in regulating downstream components of calcium signaling pathways play a role in tolerance to abiotic stresses and seed development in plants. However, functions of only a few cotton CDPKs have been clarified at present. In this study, 80 conserved CDPKs in Gossypium hirsutum L. were identified and characterized, which was divided into four subgroups. Among them, the transcript level of GhCDPK60 was significantly upregulated under drought and several hormone treatments. And we found that the expression levels of several stress-inducible genes down-regulated in GhCDPK60-silence cotton and up-regulated in GhCDPK60-overexpressing Arabidopsis. In addition, physiological analyses demonstrated that GhCDPK60 improved drought stress tolerance by improving the osmotic adjustment ability and reducing the accumulation of reactive oxygen species (ROS) in plants. These findings broaden our understanding of the biological roles of GhCDPK60 and mechanisms underlying drought stress tolerance in cotton.

Genome-wide association study reveals novel QTLs and candidate genes for seed vigor in rice

Highly seed vigor (SV) is essential for rice direct seeding (DS). Understanding the genetic mechanism of SV-related traits could contribute to increasing the efficiency of DS. However, only a few genes responsible for SV have been determined in rice, and the regulatory network of SV remains obscure. In this study, the seed germination rate (GR), seedling shoot length (SL), and shoot fresh weight (FW) related to SV traits were measured, and a genome-wide association study (GWAS) was conducted to detect high-quality loci responsible for SV using a panel of 346 diverse accessions. A total of 51 significant SNPs were identified and arranged into six quantitative trait locus (QTL) regions, including one (qGR1-1), two (qSL1-1, qSL1-2), and three (qFW1-1, qFW4-1, and qFW7-1) QTLs associated with GR, SL, and FW respectively, which were further validated using chromosome segment substitution lines (CSSLs). Integrating gene expression, gene annotation, and haplotype analysis, we found 21 strong candidate genes significantly associated with SV. In addition, the SV-related functions of LOC_Os01g11270 and LOC_Os01g55240 were further verified by corresponding CRISPR/Cas9 gene-edited mutants. Thus, these results provide clues for elucidating the genetic basis of SV control. The candidate genes or QTLs would be helpful for improving DS by molecular marker-assisted selection (MAS) breeding in rice.

Status and prospects of genome-wide association studies in cotton

Over the last two decades, the use of high-density SNP arrays and DNA sequencing have allowed scientists to uncover the majority of the genotypic space for various crops, including cotton. Genome-wide association study (GWAS) links the dots between a phenotype and its underlying genetics across the genomes of populations. It was first developed and applied in the field of human disease genetics. Many areas of crop research have incorporated GWAS in plants and considerable literature has been published in the recent decade. Here we will provide a comprehensive review of GWAS studies in cotton crop, which includes case studies on biotic resistance, abiotic tolerance, fiber yield and quality traits, current status, prospects, bottlenecks of GWAS and finally, thought-provoking question. This review will serve as a catalog of GWAS in cotton and suggest new frontiers of the cotton crop to be studied with this important tool.

Identification of miRNAs and their target genes associated with improved maize seed vigor induced by gibberellin

High seed vigor is crucial for agricultural production owing to its potential in high quality and yield of crops and a better understanding of the molecular mechanism associated with maize seed vigor is highly necessary. To better understand the involvement and regulatory mechanism of miRNAs correlated with maize seed vigor, small RNAs and degradome sequencing of two inbred lines Yu537A and Yu82 were performed. A total of 791 mature miRNAs were obtained with different expressions, among of which 505 miRNAs were newly identified and the rest miRNAs have been reported before by comparing the miRNAs with the sequences in miRbase database. Analysis of miRNA families showed maize seeds contain fewer miRNA families and larger miRNA families compared with animals, indicating that functions of miRNAs in maize seeds were more synergistic than animals. Degradome sequencing was used to identify the targets of miRNAs and the results showed a total of 6,196 targets were obtained. Function analysis of differentially expressed miRNAs and targets showed Glycan degradation and galactose metabolism were closely correlated with improved maize seed vigor. These findings provide valuable information to understand the involvement of miRNAs with maize seed vigor and these putative genes will be valuable resources for improving the seed vigor in future maize breeding.

Genetic basis of sorghum leaf width and its potential as a surrogate for transpiration efficiency

Leaf width was correlated with plant-level transpiration efficiency and associated with 19 QTL in sorghum, suggesting it could be a surrogate for transpiration efficiency in large breeding program. Enhancing plant transpiration efficiency (TE) by reducing transpiration without compromising photosynthesis and yield is a desirable selection target in crop improvement programs. While narrow individual leaf width has been correlated with greater intrinsic water use efficiency in C₄ species, the extent to which this translates to greater plant TE has not been investigated. The aims of this study were to evaluate the correlation of leaf width with TE at the whole-plant scale and investigate the genetic control of leaf width in sorghum. Two lysimetry experiments using 16 genotypes varying for stomatal conductance and three field trials using a large sorghum diversity panel (n = 701 lines) were conducted. Negative associations of leaf width with plant TE were found in the lysimetry experiments, suggesting narrow leaves may result in reduced plant transpiration without trade-offs in biomass accumulation. A wide range in width of the largest leaf was found in the sorghum diversity panel with consistent ranking among sorghum races, suggesting that environmental adaptation may have a role in modifying leaf width. Nineteen QTL were identified by genome-wide association studies on leaf width adjusted for flowering time. The QTL identified showed high levels of correspondence with those in maize and rice, suggesting similarities in the genetic control of leaf width across cereals. Three a priori candidate genes for leaf width, previously found to regulate dorsoventrality, were identified based on a 1-cM threshold. This study provides useful physiological and genetic insights for potential manipulation of leaf width to improve plant adaptation to diverse environments.

Insights into the Genomic Regions and Candidate Genes of Senescence-Related Traits in Upland Cotton via GWAS

Senescence is the last stage of plant development and is controlled by both internal and external factors. Premature senescence significantly affects the yield and quality of cotton. However, the genetic architecture underlying cotton senescence remains unclear. In this study, genome-wide association studies (GWAS) were performed based on 3,015,002 high-quality SNP markers from the resequencing data of 355 upland cotton accessions to detect genomic regions for cotton senescence. A total of 977 candidate genes within 55 senescence-related genomic regions (SGRs), SGR1-SGR55, were predicted. Gene ontology (GO) analysis of candidate genes revealed that a set of biological processes was enriched, such as salt stress, ethylene processes, and leaf senescence. Furthermore, in the leaf senescence GO term, one candidate gene was focused on: Gohir.A12G270900 (GhMKK9), located in SGR36, which encodes a protein of the MAP kinase kinase family. Quantitative real-time PCR (qRT-PCR) analysis showed that GhMKK9 was up-regulated in old cotton leaves. Overexpression of GhMKK9 in Arabidopsis accelerated natural leaf senescence. Virus-induced gene silencing (VIGS) of GhMKK9 in cotton increased drought tolerance. These results suggest that GhMKK9 is a positive regulator and might be involved in drought-induced senescence in cotton. The results provide new insights into the genetic basis of cotton senescence and will be useful for improving cotton breeding in the future.

Genomewide Identification and Characterization of the Genes Involved in the Flowering of Cotton

Flowering is a prerequisite for flowering plants to complete reproduction, and flowering time has an important effect on the high and stable yields of crops. However, there are limited reports on flowering-related genes at the genomic level in cotton. In this study, genomewide analysis of the evolutionary relationship of flowering-related genes in different cotton species shows that the numbers of flowering-related genes in the genomes of tetraploid cotton species Gossypium hirsutum and Gossypium barbadense were similar, and that these numbers were approximately twice as much as the number in diploid cotton species Gossypium arboretum. The classification of flowering-related genes shows that most of them belong to the photoperiod and circadian clock flowering pathway. The distribution of flowering-related genes on the chromosomes of the At and Dt subgenomes was similar, with no subgenomic preference detected. In addition, most of the flowering-related core genes in Arabidopsis thaliana had homologs in the cotton genome, but the copy numbers and expression patterns were disparate; moreover, flowering-related genes underwent purifying selection throughout the evolutionary and selection processes. Although the differentiation and reorganization of many key genes of the cotton flowering regulatory network occurred throughout the evolutionary and selection processes, most of them, especially those involved in the important flowering regulatory networks, have been relatively conserved and preferentially selected.

Detection of Stable Elite Haplotypes and Potential Candidate Genes of Boll Weight Across Multiple Environments via GWAS in Upland Cotton

Boll weight (BW) is a key determinant of yield component traits in cotton, and understanding the genetic mechanism of BW could contribute to the progress of cotton fiber yield. Although many yield-related quantitative trait loci (QTLs) responsible for BW have been determined, knowledge of the genes controlling cotton yield remains limited. Here, association mapping based on 25,169 single-nucleotide polymorphisms (SNPs) and 2,315 insertions/deletions (InDels) was conducted to identify high-quality QTLs responsible for BW in a global collection of 290 diverse accessions, and BW was measured in nine different environments. A total of 19 significant markers were detected, and 225 candidate genes within a 400 kb region (± 200 kb surrounding each locus) were predicted. Of them, two major QTLs with highly phenotypic variation explanation on chromosomes A08 and D13 were identified among multiple environments. Furthermore, we found that two novel candidate genes (Ghir_A08G009110 and Ghir_D13G023010) were associated with BW and that Ghir_D13G023010 was involved in artificial selection during cotton breeding by population genetic analysis. The transcription level analyses showed that these two genes were significantly differentially expressed between high-BW accession and low-BW accession during the ovule development stage. Thus, these results reveal valuable information for clarifying the genetic basics of the control of BW, which are useful for increasing yield by molecular marker-assisted selection (MAS) breeding in cotton.

Characterization and Functional Analysis of GhNAC82, A NAM Domain Gene, Coordinates the Leaf Senescence in Upland Cotton (Gossypium hirsutum L.)

In the process of growth and development, cotton exhibits premature senescence under various abiotic stresses, impairing yield and fiber quality. NAC (NAM, ATAF1,2, and CUC2) protein widely distributed in land plants, play the critical role in responding to abiotic stress and regulating leaf senescence. We have identified and functional analyzed a NAM domain gene GhNAC82 in upland cotton, it was located on the A11 chromosome 4,921,702 to 4,922,748 bp, only containing one exon. The spatio-temporal expression pattern analysis revealed that it was highly expressed in root, torus, ovule and fiber development stage. The results of qRT-PCR validated that GhNAC82 negatively regulated by salt stress, drought stress, H₂O₂ stress, IAA treatment, and ethylene treatment, positively regulated by the ABA and MeJA treatment. Moreover, heterologous overexpression of GhNAC82 results in leaf premature senescence and delays root system development in Arabidopsis thaliana. The phenotype of delayed-senescence was performed after silencing GhNAC82 by VIGS in premature cotton. Taken together, GhNAC82 was involved in different abiotic stress pathways and play important roles in negatively regulating leaf premature senescence.

GhSOC1s Evolve to Respond Differently to the Environmental Cues and Promote Flowering in Partially Independent Ways

Gossypium hirsutum is most broadly cultivated in the world due to its broader adaptation to the environment and successful breeding of early maturity varieties. However, how cotton responds to environmental cues to adjust flowering time to achieve reproductive success is largely unknown. SOC1 functions as an essential integrator for the endogenous and exogenous signals to maximize reproduction. Thus we identified six SOC1-like genes in Gossypium that clustered into two groups. GhSOC1-1 contained a large intron and clustered with monocot SOC1s, while GhSOC1-2/3 were close to dicot SOC1s. GhSOC1s expression gradually increased during seedling development suggesting their conserved function in promoting flowering, which was supported by the early flowering phenotype of 35S:GhSOC1-1 Arabidopsis lines and the delayed flowering of cotton silencing lines. Furthermore, GhSOC1-1 responded to short-day and high temperature conditions, while GhSOC1-2 responded to long-day conditions. GhSOC1-3 might function to promote flowering in response to low temperature and cold. Taken together, our results demonstrate that GhSOC1s respond differently to light and temperature and act cooperatively to activate GhLFY expression to promote floral transition and enlighten us in cotton adaptation to environment that is helpful in improvement of cotton maturity.

Transcriptional Landscape of Cotton Fiber Development and Its Alliance With Fiber-Associated Traits

Cotton fiber development is still an intriguing question to understand fiber commitment and development. At different fiber developmental stages, many genes change their expression pattern and have a pivotal role in fiber quality and yield. Recently, numerous studies have been conducted for transcriptional regulation of fiber, and raw data were deposited to the public repository for comprehensive integrative analysis. Here, we remapped > 380 cotton RNAseq data with uniform mapping strategies that span ∼400 fold coverage to the genome. We identified stage-specific features related to fiber cell commitment, initiation, elongation, and Secondary Cell Wall (SCW) synthesis and their putative cis-regulatory elements for the specific regulation in fiber development. We also mined Exclusively Expressed Transcripts (EETs) that were positively selected during cotton fiber evolution and domestication. Furthermore, the expression of EETs was validated in 100 cotton genotypes through the nCounter assay and correlated with different fiber-related traits. Thus, our data mining study reveals several important features related to cotton fiber development and improvement, which were consolidated in the "CottonExpress-omics" database.

Insights Into MicroRNA-Mediated Regulation of Flowering Time in Cotton Through Small RNA Sequencing

The timing of flowering is a key determinant for plant reproductive. It has been demonstrated that microRNAs (miRNAs) play an important role in transition from the vegetative to reproductive stage in cotton; however, knowledge remains limited about the regulatory role of miRNAs involved in flowering time regulation in cotton. To elucidate the molecular basis of miRNAs in response to flowering time in cotton, we performed high-throughput small RNA sequencing at the fifth true leaf stage. We identified 56 and 43 miRNAs that were significantly up- and downregulated in two elite early flowering cultivars (EFC) compared with two late flowering cultivars (LFC), respectively. The miRNA targets by RNA sequencing analysis showed that GhSPL4 in SBP transcription factor family targeted by GhmiR156 was significantly upregulated in EFCs. Co-expression regulatory network analysis (WGCNA) revealed that GhSOC1, GhAP1, GhFD, GhCOL3, and GhAGL16 act as node genes in the auxin- and gibberellin-mediated flowering time regulatory networks in cotton. Therefore, elucidation of miRNA-mediated flowering time regulatory network will contribute to our understanding of molecular mechanisms underlying flowering time in cotton.

High-Altitude Genetic Selection and Genome-Wide Association Analysis of Yield-Related Traits in Elymus sibiricus L. Using SLAF Sequencing

The genetic adaptations to harsh climatic conditions in high altitudes and genetic basis of important agronomic traits are poorly understood in Elymus sibiricus L. In this study, an association population of 210 genotypes was used for population structure, selective sweep analysis, and genome-wide association study (GWAS) based on 88,506 single nucleotide polymorphisms (SNPs). We found 965 alleles under the natural selection of high altitude, which included 7 hub genes involved in the response to UV, and flavonoid and anthocyanin biosynthetic process based on the protein-protein interaction (PPI) analysis. Using a mixed linear model (MLM), the GWAS test identified a total of 1,825 significant loci associated with 12 agronomic traits. Based on the gene expression data of two wheat cultivars and the PPI analysis, we finally identified 12 hub genes. Especially, in plant height traits, the top hub gene (TOPLESS protein) encoding auxins and jasmonic acid signaling pathway, shoot apical meristem specification, and xylem and phloem pattern formation was highly overexpressed. These genes might play essential roles in controlling the growth and development of E. sibiricus. Therefore, this study provides fundamental insights relevant to hub genes and will benefit molecular breeding and improvement in E. sibiricus and other Elymus species.

Identification of small effect quantitative trait loci of plant architectural, flowering, and early maturity traits in reciprocal interspecific introgression population in cotton

Plant architecture, flowering time and maturity traits are important determinants of yield and fiber quality of cotton. Genetic dissection of loci determining these yield and quality components is complicated by numerous loci with alleles conferring small differences. Therefore, mapping populations segregating for smaller numbers and sizes of introgressed segments is expected to facilitate dissection of these complex quantitative traits. At an advanced stage in the development of reciprocal advanced backcross populations from crosses between elite Gossypium hirsutum cultivar 'Acala Maxxa' (GH) and G. barbadense 'Pima S6' (GB), we undertook mapping of plant architectural traits, flowering time and maturity. A total of 284 BC₄F₁ and BC₄F₂ progeny rows, 120 in GH and 164 in GB background, were evaluated for phenotype, with only 4 and 3 (of 7) traits showing significant differences among progenies. Genotyping by sequencing yielded 3,186 and 3,026 SNPs, respectively, that revealed a total of 27 QTLs in GH background and 22 in GB, for plant height, days to flowering, residual flowering at maturity and maturity. More than of 90% QTLs identified in both backgrounds had small effects (%PV < 10), supporting the merit of this population structure to reduce background noise and small effect QTLs. Germplasm developed in this study may serve as potential pre-breeding material to develop improved cotton cultivars.

Genetic Diversity, QTL Mapping, and Marker-Assisted Selection Technology in Cotton (Gossypium spp.)

Cotton genetic resources contain diverse economically important traits that can be used widely in breeding approaches to create of high-yielding elite cultivars with superior fiber quality and adapted to biotic and abiotic stresses. Nevertheless, the creation of new cultivars using conventional breeding methods is limited by the cost and proved to be time consuming process, also requires a space to make field observations and measurements. Decoding genomes of cotton species greatly facilitated generating large-scale high-throughput DNA markers and identification of QTLs that allows confirmation of candidate genes, and use them in marker-assisted selection (MAS)-based breeding programs. With the advances of quantitative trait loci (QTL) mapping and genome-wide-association study approaches, DNA markers associated with valuable traits significantly accelerate breeding processes by replacing the selection with a phenotype to the selection at the DNA or gene level. In this review, we discuss the evolution and genetic diversity of cotton Gossypium genus, molecular markers and their types, genetic mapping and QTL analysis, application, and perspectives of MAS-based approaches in cotton breeding.

QTL and candidate gene identification of the node of the first fruiting branch (NFFB) by QTL-seq in upland cotton (Gossypium hirsutum L.)

Background

The node of the first fruiting branch (NFFB) is an important precocious trait in cotton. Many studies have been conducted on the localization of quantitative trait loci (QTLs) and genes related to fiber quality and yield, but there has been little attention to traits related to early maturity, especially the NFFB, in cotton.

Results

To identify the QTL associated with the NFFB in cotton, a BC₄F₂ population comprising 278 individual plants was constructed. The parents and two DNA bulks for high and low NFFB were whole genome sequenced, and 243.8 Gb of clean nucleotide data were generated. A total of 449,302 polymorphic SNPs and 135,353 Indels between two bulks were identified for QTL-seq. Seventeen QTLs were detected and localized on 11 chromosomes in the cotton genome, among which two QTLs (qNFFB-Dt2–1 and qNFFB-Dt3–3) were located in hotspots. Two candidate genes (GhAPL and GhHDA5) related to the NFFB were identified using quantitative real-time PCR (qRT-PCR) and virus-induced gene silencing (VIGS) experiments in this study. Both genes exhibited higher expression levels in the early-maturing cotton material RIL182 during flower bud differentiation, and the silencing of GhAPL and GhHDA5 delayed the flowering time and increased the NFFB compared to those of VA plants in cotton.

Conclusions

Our study preliminarily found that GhAPL and GhHDA5 are related to the early maturity in cotton. The findings provide a basis for the further functional verification of candidate genes related to the NFFB and contribute to the study of early maturity in cotton.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08164-2.

Non-functional GoFLA19s are responsible for the male sterility caused by hybrid breakdown in cotton (Gossypium spp.)

Hybrid breakdown (HB) functions as a common reproductive barrier and reduces hybrid fitness in many species, including cotton. However, the related genes and the underlying genetic mechanisms of HB in cotton remain unknown. Here, we found that the photosensitive genetic male sterile line CCRI9106 was a hybrid progeny of Gossypium hirsutum and Gossypium barbadense and probably a product of HB. Fine mapping with F₂ s (CCRI9106 × G. hirsutum/G. barbadense lines) identified a pair of male sterility genes GoFLA19s (encoding fasciclin-like arabinogalactan family protein) located on chromosomes A12 and D12. Crucial variations occurring in the fasciclin-like domain and the arabinogalactan protein domain were predicted to cause the non-functionalization of GbFLA19-D and GhFLA19-A. CRISPR/Cas9-mediated knockout assay confirmed the effects of GhFLA19s on male sterility. Sequence alignment analyses showed that variations in GbFLA19-D and GhFLA19-A likely occurred after the formation of allotetraploid cotton species. GoFLA19s are specifically expressed in anthers and contribute to tapetal development, exine assembly, intine formation, and pollen grain maturation. RNA-sequencing and quantitative reverse transcriptase-polymerase chain reaction analyses illustrated that genes related to these biological processes were significantly downregulated in the mutant. Our research on male sterility genes, GoFLA19s, improves the understanding of the molecular characteristics and evolutionary significance of HB in interspecific hybrid breeding.