Dataset Information

Genomic mapping and identification of candidate genes encoding nulliplex-branch trait in sea-island cotton (Gossypium barbadense L.) by multi-omics analysis.

ABSTRACT: Nulliplex branch is a key architectural trait in sea-island cotton (Gossypium barbadense L.), but its genetic basis is not well understood. Here we investigated the genetic basis of the nulliplex-branch trait in cotton by combining newly created bulked segregant analysis (BSA)-seq data, published RNA-seq data, and published whole-genome resequencing (WGR) data. We delimited the nulliplex-branch locus (qD07-NB) to D07, region 14.8-17.1 Mb, using various BSA methods and markers. We integrated our BSA data with WGR data of sea-island cotton varieties and detected a missense single-nucleotide polymorphism in the candidate gene (Gbar_D07G011870) of qD07-NB. This gene was under positive selection during sea-island cotton breeding in the Xinjiang Uygur Autonomous Region, China. Notably, the nulliplex-branch varieties possessed a better fiber quality than the long-branch varieties, and a set of high-quality molecular markers was identified for molecular breeding of the nulliplex-branch trait in cotton. We combined BSA-seq and RNA-seq data to compare gene expression profiles between two elite sea-island cotton varieties during three developmental stages. We identified eleven relevant candidate genes, five downregulated and six upregulated, in the qD07-NB locus. This research will expand our understanding of the genetic basis of the nulliplex-branch trait and provide guidance for architecture-focused breeding in cotton.

Supplementary information

The online version contains supplementary material available at 10.1007/s11032-021-01229-w.

SUBMITTER: Wen T

PROVIDER: S-EPMC10236067 | biostudies-literature | 2021 May

REPOSITORIES: biostudies-literature

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Genomic mapping and identification of candidate genes encoding nulliplex-branch trait in sea-island cotton (Gossypium barbadense L.) by multi-omics analysis.

Wen Tianwang T Liu Chunyan C Wang Tianyou T Wang Mengxing M Tang Feiyu F He Liangrong L

Molecular breeding : new strategies in plant improvement 20210518 5

Nulliplex branch is a key architectural trait in sea-island cotton (Gossypium barbadense L.), but its genetic basis is not well understood. Here we investigated the genetic basis of the nulliplex-branch trait in cotton by combining newly created bulked segregant analysis (BSA)-seq data, published RNA-seq data, and published whole-genome resequencing (WGR) data. We delimited the nulliplex-branch locus (qD07-NB) to D07, region 14.8-17.1 Mb, using various BSA methods and markers. We i ...[more]

PMID: 37309326

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Project description:BackgroundSea 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.ResultsIn 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.ConclusionsThe present study provides a foundation for genetic diversity of sea island cotton accessions and will contribute to fiber quality improvement in breeding practice.

Project description:BackgroundPlants often face multiple stresses including drought, extreme temperature, salinity, nutrition deficiency and biotic stresses during growth and development. All the stresses result in a series of physiological and metabolic reactions and then generate reversible inhibition of metabolism and growth and can cause seriously irreversible damage, even death. At each stage of cotton growth, environmental stress conditions pose devastating threats to plant growth and development, especially yield and quality. Due to the complex stress conditions and unclear molecular mechanisms of stress response, there is an urgent need to explore the mechanisms of cotton response against abiotic stresses.Methodology and principal findingsA normalized cDNA library was constructed using Gossypium barbadense Hai-7124 treated with different stress conditions (heat, cold, salt, drought, potassium and phosphorus deficit and Verticillium dahliae infection). Random sequencing of this library generated 6,047 high-quality expressed sequence tags (ESTs). The ESTs were clustered and assembled into 3,135 uniESTs, composed of 2,497 contigs and 638 singletons. The blastx results demonstrated 2,746 unigenes showing significant similarity to known genes, 74 uniESTs displaying significant similarity to genes of predicted proteins, and 315 uniESTs remain uncharacterized. Functional classification unveiled the abundance of uniESTs in binding, catalytic activity, and structural molecule activity. Annotations of the uniESTs by the plant transcription factor database (PlantTFDB) and Plant Stress Protein Database (PSPDB) disclosed that transcription factors and stress-related genes were enriched in the current library. The expression of some transcription factors and specific stress-related genes were verified by RT-PCR under various stress conditions.Conclusions/significanceAnnotation results showed that a huge number of genes respond to stress in our study, such as MYB-related, C2H2, FAR1, bHLH, bZIP, MADS, and mTERF. These results will improve our knowledge of stress tolerance in cotton. In addition, they are also helpful in discovering candidate genes related to stress tolerance. The publicly available ESTs from G. barbadense are a valuable genomic resource that will facilitate further molecular study and breeding of stress-tolerant cotton.

Project description:Verticillium wilt (VW) is a soil-borne fungal disease that is caused by Verticillium dahliae Kleb and seriously damages cotton production annually in China. To date, many efforts have been made to improve the resistance of upland cotton against VW, but little progress has been achieved because of a lack of resistant upland cotton to VW. G. barbadense is known to carry high resistance to VW; however, it is difficult to transfer the resistance trait from G. barbadense to upland cotton because of linkage drag and distortion in the interspecific hybrid. In this study, a chromosomal segment introgression line (CSIL), SuVR043, containing a single and homozygous chromosome segment of G. barbadense cv. H7124 D04 (Chr 22), was created and used to construct an F2 population for mapping of VW resistance quantitative trait loci (QTLs) in the greenhouse. Two major resistance QTLs against nondefoliating V. dahliae isolate Bp2, called qVW-Bp2-1 and qVW-Bp2-2, which were flanked by the markers cgr6409-ZHX37 and ZHX57-ZHX70 and explained an average of 16.38 and 22.36% of the observed phenotypic variation, respectively, were detected in three independent replicate experiments. The genetic distances from cgr6409 to ZHX37 and from ZHX57 to ZHX70 were 2.4 and 0.8 cM, respectively. By analyzing the genome sequence of the qVW-Bp2-1 and qVW-Bp2-2 regions, we determined that the accurate physical distances from cgr6409 to ZHX37 and from ZHX57 to ZHX70 in the G. barbadense genome are 254 and 140 kb, and that those spans 36 and 20 putative genes, respectively. The results of the expression analysis showed significant differences in the expression profiles of GbCYP450, GbTMEM214, and GbRLK among G. barbadense cv. H7124, CSIL SuVR043 and G. hirsutum acc. Sumian 8 at different times after inoculation with V. dahliae isolate Bp2. Virus-induced gene silencing (VIGS) analysis showed that silencing of GbCYP450 and GbTMEM214 decreased H7124 and CSIL SuVR043 resistance to VW. These results form a solid foundation for fine mapping and cloning of resistance genes in the substituted segment and will provide valuable assistance in future efforts to breed for VW resistance.

Dataset Information

Genomic mapping and identification of candidate genes encoding nulliplex-branch trait in sea-island cotton (Gossypium barbadense L.) by multi-omics analysis.

Supplementary information

Publications

Genomic mapping and identification of candidate genes encoding nulliplex-branch trait in sea-island cotton (<i>Gossypium barbadense</i> L.) by multi-omics analysis.

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