Identification of candidate genes involved in salt stress response at germination and seedling stages by QTL mapping in upland cotton
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ABSTRACT:
PROVIDER: PRJNA774289 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR16569100_1.fastq.gz | Fastqsanger.gz | |||
| SRR16569100_2.fastq.gz | Fastqsanger.gz | |||
| SRR16569101_1.fastq.gz | Fastqsanger.gz | |||
| SRR16569101_2.fastq.gz | Fastqsanger.gz | |||
| SRR16569102_1.fastq.gz | Fastqsanger.gz |
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Project description:Salinity is a major abiotic stress at critical stages of seed germination and seedling establishment. Germination rate (GR) and field emergence rate (FER) are the key traits that determine the basic number of plants stand under field conditions. To explore molecular mechanisms in upland cotton under salt stress, a population of 177 recombinant inbred lines (RILs) and their parents were evaluated for seed germination traits (GP, germination potential; GR; FW, fresh weight; DW, dry weight; GL, germinal length) and seedling traits (FER; SH, seedling height; NL, Number of main stem leaves) in 2016-2018. Based on the linkage map contained 2,859 single nucleotide polymorphism (SNP) and simple sequence repeats (SSR) markers, traits under salt stress (E1) and normal condition, (E2) and the converted relative index (R-value) of three years’ trials were used to map quantitative trait loci (QTL). A total of three QTL and two clusters were detected as salt-tolerant QTL. Three QTL (qGR-Chr4-3, qFER-Chr12-3, qFER-Chr15-1) were detected under salt stress and R-value, which explained phenotypic variance of 9.62%-13.67%, and 4.2%-4.72%, 4.75%-8.96%, respectively. Two clusters (Loci-Chr4-2 and Loci-Chr5-4) harboring the QTL for four germination traits (GR, FER, GL, NL) and six seedling traits (GR, FER, DW, FW, SH, NL) were detected related under salt stress. A total of 691 genes were found in the candidate QTL or clusters. Among them, four genes (Gh_A04G1106, Gh_A05G3246, Gh_A05G3177, Gh_A05G3266) showed expression changes between sensitive and tolerant lines under salt stress, and were assigned as candidate genes in response to salt stress. The consistent salt-tolerance QTL identified in both germination and seedling stages will facilitate new information for cotton breeding.
2022-06-23 | GSE186533 | GEO
Project description:Salinity is a major abiotic stress at critical stages of seed germination and seedling establishment. Germination rate (GR) and field emergence rate (FER) are the key traits that determine the basic number of plants stand under field conditions. To explore molecular mechanisms in upland cotton under salt stress, a population of 177 recombinant inbred lines, and their parents were evaluated for seed germination traits (GP, germination potential; GR; FW, fresh weight; DW, dry weight; GL, germinal length) and seedling traits (FER; SH, seedling height; NL, number of main stem leaves) in 2016-2018. Based on the linkage map contained 2,859 single nucleotide polymorphism and simple sequence repeat markers, traits under salt stress (E1) and normal conditions (E2), and in the converted relative index (R-value) dataset of 3 years' trials were used to map quantitative trait loci (QTL). A total of 3 QTL and 2 clusters were detected as salt-tolerant QTL. Three QTL (qGR-Chr4-3, qFER-Chr12-3, and qFER-Chr15-1) were detected under salt stress conditions and R-value dataset, which explained variance of phenotype 9.62-13.67%, and 4.2-4.72%, 4.75-8.96%, respectively. Two clusters (Loci-Chr4-2 and Loci-Chr5-4) harboring the QTL for 4 germination traits (GR, FER, GL, and NL) and 6 seedling traits (GR, FER, DW, FW, SH, and NL) were detected related under salt stress. A total of 691 genes were found in the candidate QTL or clusters. Among them, 4 genes (Gh_A04G1106, Gh_A05G3246, Gh_A05G3177, and Gh_A05G3266) showed expression differences between salt-sensitive and -tolerant lines under salt stress conditions, and were assigned as candidate genes in response to salt stress. The consistent salt-tolerance QTL identified in both germination and seedling stages will facilitate novel insights into effective utilization of cotton genetic resources.
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Project description:Sorghum (Sorghum bicolor L.) a drought tolerant staple crop for half a billion people in Africa and Asia, an important source of animal feed throughout the world and a biofuel feedstock of growing importanceorghum's originated from tropical regions rendering the crop to be cold sensitive. Low temperature stresses such as chilling and frost greatly affect the agronomic performance of sorghum and limit its geographical distribution, posing a major problem in temperate environments when sorghum is planted early. Understanding the genetic basis of wide adaptability and of sorghum would facilitate molecular breeding programs and studies of other C4 crops. The objective of this study is to conduct quantitative trait loci analysis using genotying by sequencing for early seed germination and seedling cold tolerance in two sorghum recombinant inbred lines populations. To accomplish that, we used two populations of recombinant inbred lines (RIL) developed from crosses between cold-tolerant (CT19, ICSV700) and cold-sensitive (TX430, M81E) parents. The derived RIL populations were evaluated for single nucleotide polymorphism (SNP) using genotype-by-sequencing (GBS) in the field and under controlled environments for their response to chilling stress. Linkage maps were constructed with 464 and 875 SNPs for the CT19 X TX430 (C1) and ICSV700 X M81 E (C2) populations respectively. Using quantitative trait loci (QTL) mapping, we identified QTL conferring tolerance to chilling tolerance at the seedling stage. A total of 16 and 39 total QTL were identified in the C1 and C2 populations, respectively. Two major QTL were identified in the C1 population, and three major QTL were mapped in the C2 population. Comparisons between the two populations and with previously identified QTL show a high degree of similarity in QTL locations. Given the amount of co-localization of QTL across traits and the direction of allelic effect supports that these regions have a pleiotropic effect. These QTL regions were also identified to be highly enriched for genes encoding chilling stress and hormonal response genes. This identified QTL can be useful in developing tools for molecular breeding of sorghums with improved low-temperature germinability.
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Project description:Improving cotton yield is a major breeding goal for Chinese upland cotton. Lint percentage is an important yield component and a critical economic index for cotton cultivars, and raising the lint percentage has a close relationship to improving cotton lint yield. To investigate the genetic architecture of lint percentage, a diversity panel consisting of 355 upland cotton accessions was grown, and the lint percentage was measured in four different environments. Genotyping was performed with specific-locus amplified fragment sequencing (SLAF-seq). Twelve single-nucleotide polymorphisms (SNPs) associated with lint percentage were detected via a genome-wide association study (GWAS), in which five SNP loci distributed on chromosomes At3 (A02) and At4 (A08) and contained two major-effect QTLs, which were detected in the best linear unbiased predictions (BLUPs) and in more than three environments simultaneously. Furthermore, favorable haplotypes (FHs) of two major-effect QTLs and 47 putative candidate genes in the two linkage disequilibrium (LD) blocks of these associated loci were identified. The expression levels of these putative candidate genes were estimated using RNA-seq data from ten upland cotton tissues. We found that Gh_A02G1268 was very highly expressed during the early fiber development stage, whereas the gene was poorly expressed in the seed. These results implied that Gh_A02G1268 may determine the lint percentage by regulating seed and fiber development. The favorable QTL alleles and candidate genes for lint percentage identified in this study will have high potential for improving lint yield in future Chinese cotton breeding programs.
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