Genome-wide association reveals genetic variation of lint yield components under salty field conditions in cotton (Gossypium hirsutum L.)

Yield-related quantitative trait loci identification and lint percentage hereditary dissection under salt stress in upland cotton

Salinity is frequently mentioned as a major constraint in worldwide agricultural production. Lint percentage (LP) is a crucial yield-component in cotton lint production. While the genetic factors affect cotton yield in saline soils are still unclear. Here, we employed a recombinant inbred line population in upland cotton (Gossypium hirsutum L.) and investigated the effects of salt stress on five yield and yield component traits, including seed cotton yield per plant, lint yield per plant, boll number per plant, boll weight, and LP. Between three datasets of salt stress (E1), normal growth (E2), and the difference values dataset of salt stress and normal conditions (D-value), 87, 82, and 55 quantitative trait loci (QTL) were detectable, respectively. In total, five QTL (qLY-Chr6-2, qBNP-Chr4-1, qBNP-Chr12-1, qBNP-Chr15-5, qLP-Chr19-2) detected in both in E1 and D-value were salt related QTL, and three stable QTL (qLP-Chr5-3, qLP-Chr13-1, qBW-Chr5-5) were detected both in E1 and E2 across 3 years. Silencing of nine genes within a stable QTL (qLP-Chr5-3) highly expressed in fiber developmental stages increased LP and decreased fiber length (FL), indicating that multiple minor-effect genes clustered on Chromosome 5 regulate LP and FL. Additionally, the difference in LP caused by Gh_A05G3226 is mainly in transcription level rather than in the sequence difference. Moreover, silencing of salt related gene (GhDAAT) within qBNP-Chr4-1 decreased salt tolerance in cotton. Our findings shed light on the regulatory mechanisms underlining cotton salt tolerance and fiber initiation.

Genome-wide association study for boll weight in Gossypium hirsutum races

High yield has always been an essential target in almost all of the cotton breeding programs. Boll weight (BW) is a key component of cotton yield. Numerous linkage mapping and genome-wide association studies (GWAS) have been performed to understand the genetic mechanism of BW, but information on the markers/genes controlling BW remains limited. In this study, we conducted a GWAS for BW using 51,268 high-quality single-nucleotide polymorphisms (SNPs) and 189 Gossypium hirsutum accessions across five different environments. A total of 55 SNPs significantly associated with BW were detected, of which 29 and 26 were distributed in the A and D subgenomes, respectively. Five SNPs were simultaneously detected in two environments. For TM5655, TM8662, TM36371, and TM50258, the BW grouped by alleles of each SNP was significantly different. The ± 550 kb regions around these four key SNPs contained 262 genes. Of them, Gh_A02G1473, Gh_A10G1765, and Gh_A02G1442 were expressed highly at 0 to 1 days post-anthesis (dpa), - 3 to 0 dpa, and - 3 to 0 dpa in ovule of TM-1, respectively. They were presumed as the candidate genes for fiber cell differentiation, initiation, or elongation based on gene annotation of their homologs. Overall, these results supplemented valuable information for dissecting the genetic architecture of BW and might help to improve cotton yield through molecular marker-assisted selection breeding and molecular design breeding.

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

KEY MESSAGE

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

Genome-Wide Association Study of Lint Percentage in Gossypium hirsutum L. Races

Lint percentage is one of the most essential yield components and an important economic index for cotton planting. Improving lint percentage is an effective way to achieve high-yield in cotton breeding worldwide, especially upland cotton (Gossypium hirsutum L.). However, the genetic basis controlling lint percentage has not yet been systematically understood. Here, we performed a genome-wide association mapping for lint percentage using a natural population consisting of 189 G. hirsutum accessions (188 accessions of G. hirsutum races and one cultivar TM-1). The results showed that 274 single-nucleotide polymorphisms (SNPs) significantly associated with lint percentage were detected, and they were distributed on 24 chromosomes. Forty-five SNPs were detected at least by two models or at least in two environments, and their 5 Mb up- and downstream regions included 584 makers related to lint percentage identified in previous studies. In total, 11 out of 45 SNPs were detected at least in two environments, and their 550 Kb up- and downstream region contained 335 genes. Through RNA sequencing, gene annotation, qRT-PCR, protein-protein interaction analysis, the cis-elements of the promotor region, and related miRNA prediction, Gh_D12G0934 and Gh_A08G0526 were selected as key candidate genes for fiber initiation and elongation, respectively. These excavated SNPs and candidate genes could supplement marker and gene information for deciphering the genetic basis of lint percentage and facilitate high-yield breeding programs of G. hirsutum ultimately.

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

BACKGROUND

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

RESULTS

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

CONCLUSIONS

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

Genome-Wide Association Mapping Identifies New Candidate Genes for Cold Stress and Chilling Acclimation at Seedling Stage in Rice (Oryza sativa L.)

Rice (Oryza sativa L.) is a chilling-sensitive staple food crop, and thus, low temperature significantly affects rice growth and yield. Many studies have focused on the cold shock of rice although chilling acclimation is more likely to happen in the field. In this paper, a genome-wide association study (GWAS) was used to identify the genes that participated in cold stress and chilling accumulation. A total of 235 significantly associated single-nucleotide polymorphisms (SNPs) were identified. Among them, we detected 120 and 88 SNPs for the relative shoot fresh weight under cold stress and chilling acclimation, respectively. Furthermore, 11 and 12 quantitative trait loci (QTLs) were identified for cold stress and chilling acclimation, respectively, by integrating the co-localized SNPs. Interestingly, we identified 10 and 15 candidate genes in 11 and 12 QTLs involved in cold stress and chilling acclimation, respectively, and two new candidate genes (LOC_Os01g62410, LOC_Os12g24490) were obviously up-regulated under chilling acclimation. Furthermore, OsMYB3R-2 (LOC_Os01g62410) that encodes a R1R2R3 MYB gene was associated with cold tolerance, while a new C3HC4-type zinc finger protein-encoding gene LOC_Os12g24490 was found to function as a putative E3 ubiquitin-protein ligase in rice. Moreover, haplotype, distribution, and Wright’s fixation index (FST) of both genes showed that haplotype 3 of LOC_Os12g24490 is more stable in chilling acclimation, and the SNP (A > T) showed a difference in latitudinal distribution. FST analysis of SNPs in OsMYB3R-2 (LOC_Os01g62410) and LOC_Os12g24490 indicated that several SNPs were under selection in rice indica and japonica subspecies. This study provided new candidate genes in genetic improvement of chilling acclimation response 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.

Global identification of quantitative trait loci and candidate genes for cold stress and chilling acclimation in rice through GWAS and RNA-seq

Associated analysis of GWAS with RNA-seq had detected candidate genes responsible for cold stress and chilling acclimation in rice. Haplotypes of two candidate genes and geographic distribution were analyzed. To explore new candidate genes and genetic resources for cold tolerance improvement in rice, genome-wide association study (GWAS) mapping experiments with 351 rice core germplasms was performed for three traits (survival rate, shoot length and chlorophyll content) under three temperature conditions (normal temperature, cold stress and chilling acclimation), yielding a total of 134 QTLs, of which 54, 59 and 21 QTLs were responsible for normal temperature, cold stress and chilling acclimation conditions, respectively. Integrated analysis of significant SNPs in 134 QTLs further identified 116 QTLs for three temperature treatments, 53, 43 and 18 QTLs responsible for normal temperature, cold stress and chilling acclimation, respectively, and 2 QTLs were responsible for both cold stress and chilling acclimation. Matching differentially expressed genes from RNA-seq to 43 and 18 QTLs for cold stress and chilling acclimation, we identified 69 and 44 trait-associated candidate genes, respectively, to be classified into six and five groups, particularly involved in metabolisms, reactive oxygen species scavenging and hormone signaling. Interestingly, two candidate genes LOC_Os01g04814, encoding a vacuolar protein sorting-associating protein 4B, and LOC_Os01g48440, encoding glycosyltransferase family 43 protein, showed the highest expression levels under chilling acclimation. Haplotype analysis revealed that both genes had a distinctive differentiation with subpopulation. Haplotypes of both genes with more japonica accessions have higher latitude distribution and higher chilling tolerance than the chilling sensitive indica accessions. These findings reveal the new insight into the molecular mechanism and candidate genes for cold stress and chilling acclimation in rice.

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

Thirty-four SNPs corresponding with 22 QTLs for lint percentage, including 13 novel QTLs, was detected via GWAS. Two candidate genes underlying this trait were also identified. Cotton (Gossypium spp.) is an important natural textile fiber and oilseed crop cultivated worldwide. Lint percentage (LP, %) is one of the important yield components, and increasing LP is a core goal of cotton breeding improvement. However, the genetic and molecular mechanisms underlying LP in upland cotton remain unclear. Here, we performed a genome-wide association study (GWAS) for LP based on 254 upland cotton accessions in four environments as well as the best linear unbiased predictors using the high-density CottonSNP80K array. In total, 41,413 high-quality single-nucleotide polymorphisms (SNPs) were screened, and 34 SNPs within 22 quantitative trait loci (QTLs) were significantly associated with LP. In total, 175 candidate genes were identified from two major genomic loci (GR1 and GR2), and 50 hub genes were identified through GO enrichment and weighted gene co-expression network analysis. Two candidate genes (Gh_D01G0162 and Gh_D07G0463), which may participate in early fiber development to affect the number of fiber protrusions and LP, were also identified. Their genetic variation and expression were verified by linkage disequilibrium blocks, haplotypes, and quantitative real-time polymerase chain reaction, respectively. The weighted gene interaction network analysis showed that the expression of Gh_D07G0463 was significantly correlated with that of Gh_D01G0162. These identified SNPs, QTLs and candidate genes provide important insights into the genetic and molecular mechanisms underlying variations in LP and serve as a foundation for LP improvement via marker-assisted breeding.

Inheritance, QTLs, and Candidate Genes of Lint Percentage in Upland Cotton

Cotton (Gossypium spp.) is an important natural fiber plant. Lint percentage (LP) is one of the most important determinants of cotton yield and is a typical quantitative trait with high variation and heritability. Many cotton LP genetic linkages and association maps have been reported. This work summarizes the inheritance, quantitative trait loci (QTLs), and candidate genes of LP to facilitate LP genetic study and molecular breeding. More than 1439 QTLs controlling LP have been reported. Excluding replicate QTLs, 417 unique QTLs have been identified on 26 chromosomes, including 243 QTLs identified at LOD >3. More than 60 are stable, major effective QTLs that can be used in marker-assisted selection (MAS). More than 90 candidate genes for LP have been reported. These genes encode MYB, HOX, NET, and other proteins, and most are preferentially expressed during fiber initiation and elongation. A putative molecular regulatory model of LP was constructed and provides the foundation for the genetic study and molecular breeding of LP.

Ion homeostasis and Na+ transport-related gene expression in two cotton (Gossypium hirsutum L.) varieties under saline, alkaline and saline-alkaline stresses

The sensitivity of cotton to salt stress depends on the genotypes and salt types. Understanding the mechanism of ion homeostasis under different salt stresses is necessary to improve cotton performance under saline conditions. A pot experiment using three salt stresses saline stress (NaCl+Na2SO4), alkaline stress (Na2CO3+NaHCO3), and saline-alkaline stress (NaCl+Na2SO4+Na2CO3+NaHCO3) and two cotton varieties (salt-tolerant variety L24 and salt-sensitive variety G1) was conducted. The growth, ion concentrations, and Na+ transport-related gene expression in the cotton varieties were determined. The inhibitory effects of saline-alkaline stress on cotton growth were greater than that of either saline stress or alkaline stress alone. The root/shoot ratio under alkaline stress was significantly lower than that under saline stress. The salt-tolerant cotton variety had lower Na and higher K concentrations in the leaves, stems and roots than the salt-sensitive variety under different salt stresses. For the salt-sensitive cotton variety, saline stress significantly inhibited the absorption of P and the transport of P, K, and Mg, while alkaline stress and saline-alkaline stress significantly inhibited the uptake and transport of P, K, Ca, Mg, and Zn. Most of the elements in the salt-tolerant variety accumulated in the leaves and stems under different salt stresses. This indicated that the salt-tolerant variety had a stronger ion transport capacity than the salt-sensitive variety under saline conditions. Under alkaline stress and salt-alkaline stress, the relative expression levels of the genes GhSOS1, GhNHX1 and GhAKT1 in the salt-tolerant variety were significantly higher than that in the salt-sensitive variety. These results suggest that this salt-tolerant variety of cotton has an internal mechanism to maintain ionic homeostasis.

Genome-wide association analysis reveals quantitative trait loci and candidate genes involved in yield components under multiple field environments in cotton (Gossypium hirsutum)

BACKGROUND

Numerous quantitative trait loci (QTLs) and candidate genes associated with yield-related traits have been identified in cotton by genome-wide association study (GWAS) analysis. However, most of the phenotypic data were from a single or few environments, and the stable loci remained to be validated under multiple field environments.

RESULTS

Here, 242 upland cotton accessions collected from different origins were continuously investigated for phenotypic data of four main yield components, including boll weight (BW) and lint percentage (LP) under 13 field environments, and boll number per plant (BN) and seed index (SI) under 11 environments. Correlation analysis revealed a positive correlation between BN and LP, BW and SI, while SI had a negative correlation with LP and BN. Genetic analysis indicated that LP had the highest heritability estimates of 94.97%, followed by 92.08% for SI, 86.09% for BW, and 72.92% for BN, indicating LP and SI were more suitable traits for genetic improvement. Based on 56,010 high-quality single nucleotide polymorphisms (SNPs) and GWAS analysis, a total of 95 non-redundant QTLs were identified, including 12 of BN, 23 of BW, 45 of LP, and 33 of SI, respectively. Of them, 10 pairs of homologous QTLs were detected between A and D sub-genomes. We also found that 15 co-located QTLs with more than two traits and 12 high-confidence QTLs were detected under more than six environments, respectively. Further, two NET genes (GH_A08G0716 and GH_A08G0783), located in a novel QTL hotspot (qtl24, qtl25 and qlt26) were predominately expressed in early fiber development stages, exhibited significant correlation with LP and SI. The GH_A07G1389 in the stable qtl19 region encoded a tetratricopeptide repeat (TPR)-like superfamily protein and was a homologous gene involved in short fiber mutant ligon lintless-y (Li_y), implying important roles in cotton yield.

CONCLUSIONS

The present study provides a foundation for understanding the regulatory mechanisms of yield components and may enhance yield improvement through molecular breeding in cotton.

Genome-wide association analysis reveals genetic variations and candidate genes associated with salt tolerance related traits in Gossypium hirsutum

Background

Cotton is more resistant to salt and drought stresses as compared to other field crops, which makes itself as a pioneer industrial crop in saline-alkali lands. However, abiotic stresses still negatively affect its growth and development significantly. It is therefore important to breed salt tolerance varieties which can help accelerate the improvement of cotton production. The development of molecular markers linked to causal genes has provided an effective and efficient approach for improving salt tolerance.

Results

In this study, a genome-wide association study (GWAS) of salt tolerance related traits at seedling stage was performed based on 2 years of phenotype identification for 217 representative upland cotton cultivars by genotyping-by-sequencing (GBS) platform. A total of 51,060 single nucleotide polymorphisms (SNPs) unevenly distributed among 26 chromosomes were screened across the cotton cultivars, and 25 associations with 27 SNPs scattered over 12 chromosomes were detected significantly (−log₁₀^p > 4) associated with three salt tolerance related traits in 2016 and 2017. Among these, the associations on chromosome A13 and D08 for relative plant height (RPH), A07 for relative shoot fresh matter weight (RSFW), A08 and A13 for relative shoot dry matter weight (RSDW) were expressed in both environments, indicating that they were likely to be stable quantitative trait loci (QTLs). A total of 12 salt-induced candidate genes were identified differentially expressed by the combination of GWAS and transcriptome analysis. Three promising genes were selected for preliminary function verification of salt tolerance. The increase of GH_A13G0171-silenced plants in salt related traits under salt stress indicated its negative function in regulating the salt stress response.

Conclusions

These results provided important genetic variations and candidate genes for accelerating the improvement of salt tolerance in cotton.

Genome-wide association analysis reveals genetic variations and candidate genes associated with salt tolerance related traits in Gossypium hirsutum

BACKGROUND

Cotton is more resistant to salt and drought stresses as compared to other field crops, which makes itself as a pioneer industrial crop in saline-alkali lands. However, abiotic stresses still negatively affect its growth and development significantly. It is therefore important to breed salt tolerance varieties which can help accelerate the improvement of cotton production. The development of molecular markers linked to causal genes has provided an effective and efficient approach for improving salt tolerance.

RESULTS

In this study, a genome-wide association study (GWAS) of salt tolerance related traits at seedling stage was performed based on 2 years of phenotype identification for 217 representative upland cotton cultivars by genotyping-by-sequencing (GBS) platform. A total of 51,060 single nucleotide polymorphisms (SNPs) unevenly distributed among 26 chromosomes were screened across the cotton cultivars, and 25 associations with 27 SNPs scattered over 12 chromosomes were detected significantly (-log₁₀^p > 4) associated with three salt tolerance related traits in 2016 and 2017. Among these, the associations on chromosome A13 and D08 for relative plant height (RPH), A07 for relative shoot fresh matter weight (RSFW), A08 and A13 for relative shoot dry matter weight (RSDW) were expressed in both environments, indicating that they were likely to be stable quantitative trait loci (QTLs). A total of 12 salt-induced candidate genes were identified differentially expressed by the combination of GWAS and transcriptome analysis. Three promising genes were selected for preliminary function verification of salt tolerance. The increase of GH_A13G0171-silenced plants in salt related traits under salt stress indicated its negative function in regulating the salt stress response.

CONCLUSIONS

These results provided important genetic variations and candidate genes for accelerating the improvement of salt tolerance in cotton.

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.

Temporal salt stress-induced transcriptome alterations and regulatory mechanisms revealed by PacBio long-reads RNA sequencing in Gossypium hirsutum

Background

Cotton (Gossypium hirsutum) is considered a fairly salt tolerant crop however, salinity can still cause significant economic losses by affecting the yield and deteriorating the fiber quality. We studied a salt-tolerant upland cotton cultivar under temporal salt stress to unfold the salt tolerance molecular mechanisms. Biochemical response to salt stress (400 mM) was measured at 0 h, 3 h, 12 h, 24 h and 48 h post stress intervals and single-molecule long-read sequencing technology from Pacific Biosciences (PacBio) combined with the unique molecular identifiers approach was used to identify differentially expressed genes (DEG).

Results

Antioxidant enzymes including, catalase (CAT), peroxidase (POD), superoxide dismutase (SOD) were found significantly induced under temporal salt stress, suggesting that reactive oxygen species scavenging antioxidant machinery is an essential component of salt tolerance mechanism in cotton. We identified a wealth of novel transcripts based on the PacBio long reads sequencing approach. Prolonged salt stress duration induces high number of DEGs. Significant numbers of DEGs were found under key terms related to stress pathways such as “response to oxidative stress”, “response to salt stress”, “response to water deprivation”, “cation transport”, “metal ion transport”, “superoxide dismutase”, and “reductase”. Key DEGs related to hormone (abscisic acid, ethylene and jasmonic acid) biosynthesis, ion homeostasis (CBL-interacting serine/threonine-protein kinase genes, calcium-binding proteins, potassium transporter genes, potassium channel genes, sodium/hydrogen exchanger or antiporter genes), antioxidant activity (POD, SOD, CAT, glutathione reductase), transcription factors (myeloblastosis, WRKY, Apetala 2) and cell wall modification were found highly active in response to salt stress in cotton. Expression fold change of these DEGs showed both positive and negative responses, highlighting the complex nature of salt stress tolerance mechanisms in cotton.

Conclusion

Collectively, this study provides a good insight into the regulatory mechanism under salt stress in cotton and lays the foundation for further improvement of salt stress tolerance.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-020-07260-z.

Effects of Environment and Sowing Time on Growth and Yield of Upland Cotton (Gossypium hirsutum L.) Cultivars in Sicily (Italy)

Cotton is one of the most important industrial crops in the world. Though widely cultivated in Sicily (Italy) in the past, cotton growth on the island has disappeared today due to a complex variety of agronomic, economic and socio-political reasons. In recent years, increased interest in natural fibers worldwide has led to a revival in cotton plants in the Mediterranean area. The aim of this paper was to assess the response of Gossypium hirsutum L. cultivars to different environments and sowing times. Elsa and Juncal were selected from the most promising cotton cultivars regarding earliness and productivity. Plants were tested with three sowing times and in two Sicilian environments. Cotton yield and yield components were significantly affected by experimental station, sowing time and cultivar. Lint yield of cultivars was 1.60 t ha⁻¹ on average, and the highest value of 1.99 t ha⁻¹ was obtained from an early sowing time. The three indices of agronomic earliness varied significantly based on treatments. In conclusion, the evaluation of response genotype-by-environment under different sowing times could represent a strategy to obtain optimal cotton seed and lint yields, although other general aspects, such as labor costs, land availability and capital resources, should be also considered when evaluating the reintroduction of the species in Sicily.

Genome-wide association analysis reveals loci and candidate genes involved in fiber quality traits in sea island cotton (Gossypium barbadense)

BACKGROUND

Sea island cotton (Gossypium barbadense) has markedly superior high quality fibers, which plays an important role in the textile industry and acts as a donor for upland cotton (G. hirsutum) fiber quality improvement. The genetic characteristics analysis and the identification of key genes will be helpful to understand the mechanism of fiber development and breeding utilization in sea island cotton.

RESULTS

In this study, 279 sea island cotton accessions were collected from different origins for genotyping and phenotyping fiber quality traits. A set of 6303 high quality single nucleotide polymorphisms (SNPs) were obtained by high-density CottonSNP80K array. The population characteristics showed that the sea island cotton accessions had wide genetic diversity and were clustered into three groups, with Group1 closely related to Menoufi, an original sea island cotton landrace, and Group2 and Group3 related to widely introduced accessions from Egypt, USA and Former Soviet Union. Further, we used 249 accessions and evaluated five fiber quality traits under normal and salt environments over 2 years. Except for fiber uniformity (FU), fiber length (FL) and fiber elongation (FE) were significantly decreased in salt conditions, while fiber strength (FS) and fiber micronaire (MIC) were increased. Based on 6303 SNPs and genome-wide association study (GWAS) analysis, a total of 34 stable quantitative trait loci (QTLs) were identified for the five fiber quality traits with 25 detected simultaneously under normal and salt environments. Gene Ontology (GO) analysis indicated that candidate genes in the 25 overlapped QTLs were enriched mostly in "cellular and biological process". In addition, "xylem development" and "response to hormone" pathways were also found. Haplotype analyses found that GB_A03G0335 encoding an E3 ubiquitin-protein ligase in QTL TM6004 had SNP variation (A/C) in gene region, was significantly correlated with FL, FS, FU, and FE, implying a crucial role in fiber quality.

CONCLUSIONS

The present study provides a foundation for genetic diversity of sea island cotton accessions and will contribute to fiber quality improvement in breeding practice.