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Genes, SNP markers and their applications significantly correlated with cotton clothing traits

A cotton and labeling technology, applied in recombinant DNA technology, microbial determination/inspection, DNA/RNA fragments, etc., can solve the problems of affecting lint traits, limited research on the genetic basis of lint traits, etc., and achieve the effect of convenient detection

Active Publication Date: 2020-10-27
INST OF COTTON RES CHINESE ACAD OF AGRI SCI
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

Furthermore, through bioinformatics analysis, it was found that Gh_D08G2376 is homologous to AT3G07020 and GhSGT1 genes, and it is speculated that Gh_D08G2376 may affect the traits of clothing by regulating seed size and fiber development.
In general, research on the genetic basis of clothing traits is relatively limited, and further research is needed

Method used

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  • Genes, SNP markers and their applications significantly correlated with cotton clothing traits
  • Genes, SNP markers and their applications significantly correlated with cotton clothing traits
  • Genes, SNP markers and their applications significantly correlated with cotton clothing traits

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Experimental program
Comparison scheme
Effect test

Embodiment 1

[0051] 1. Materials and methods

[0052] Selection of experimental materials and design of field experiments

[0053] In this study, we mainly collected representative cotton varieties that have played an important role in different historical stages from the national mid-term bank of cotton germplasm resources of the Cotton Research Institute of the Chinese Academy of Agricultural Sciences and the breedings accumulated in the long-term high-yield breeding practice of our research team. Basic materials, a total of 276 upland cotton materials, are used for subsequent correlation analysis.

[0054] These materials can be divided into five categories according to their geographical origin: Yellow River Valley varieties (YRR), Yangtze River Valley varieties (YtRR), Northwest Inland River Valley materials (NW), Northern early-maturing varieties (NSEMR) and varieties from other countries in the world. All materials were planted at five sites in 2016-2017. Namely: Anyang, Henan (20...

Embodiment 2

[0067] The DNA of the young leaf tissue of each material was extracted by the modified CTAB method. Materials were genotyped using the CottonSNP63K chip. GenomeStudio v2011.1 analysis software was used for quality control of SNP typing results. Then, the SNPs were further screened according to the criteria of call rate>85% and minimum allele frequency (MAF)>0.05. Finally, the SNP probe sequence was compared with the upland cotton reference genome TM-1 (Gossypium hirsutum (AD1) GenomeNAU-NBI Assembly v1.1&Annotation v1.1) to obtain the physical location of the SNP.

[0068] The alignment results showed that 14,977 SNPs were aligned to the scaffold region where the staining position was not determined, and 48,081 SNPs were aligned to the chromosome. These SNPs aligned to the chromosome will be used for further analysis. Then, according to the set filtering criteria, call rate>85% and MAF>0.05. Finally, 10660 high-quality SNPs were obtained and used in subsequent correlation a...

Embodiment 3

[0074] Based on the Bayesian model in STRUCTURE 2.3.4 software, the population structure analysis of 276 upland cotton materials was carried out. The number of groups (K) is set to 1-10, among which the Length of burn-in period (Length of burn-in period) is set to 10000, the Monte Carlo iteration (Marko chain monte carlo, MCMC) is set to 100000, and each K value is independent Run 5 times. Then, referring to the method of Evanno et al., the optimal number of subpopulations of the population was estimated according to the LnP(K) and ΔK values. The results of five runs of the optimal K value were integrated using CLUMPP software to obtain the population structure matrix (Q matrix). In addition, principal component analysis (PCA) and kinship analysis were performed using the GAPIT software package. Using PowerMarker v3.25 software to calculate polymorphic information content (Polymorphic information content, PIC), gene diversity (Gene diversity) and Nei's genetic distance. The...

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Abstract

The invention relates to the field of molecular biology of characters of fiber yield, in particular to a gene in significant correlation with the characters of the fiber yield, a SNP marker and application of theSNP marker. The gene in significant correlation with the characters of the fiber yield is a Gh_D05G1124 gene and / or a Gh_D05G0313 gene. 276 upland cotton materials are taken as raw materials and planted in multiple environments, a CottonSNP63k gene chip is adopted for genetic typing, and 10660 high-quality SNPs are obtained and used for analyzing of the genetic structureand GWAS. According to the result, 23 SNPs in significant correlation with the characters of the fiber yield are discovered to correspond to 15 QTLs. In addition, through Qrt-PCR analyzing, the Gh_D05G1124 gene andthe Gh_D05G0313 gene are taken as candidate genes for adjusting the characters of the fiber yield, the SNP marker in significant correlation with the fiber yield is obtained, and theoretical support is provided for research and application of the characters of the fiber yield.

Description

technical field [0001] The invention relates to the field of molecular biology of cotton clothing properties, in particular, relates to genes significantly related to cotton clothing properties, SNP markers and applications thereof. Background technique [0002] Cotton is the main source of natural textile fibers and an important economic crop in the world. Upland cotton (Gossypium hirsutum L.), an allotetraploid cotton species, accounts for about 95% of global cotton production. Increasing cotton yield has always been an important goal of cotton breeding work. Among them, lint yield is an important indicator to measure cotton yield, which is composed of boll number per plant, clothing percentage, and boll weight per plant. Numerous studies have found that there is a significant positive correlation between coat content and cotton yield, and coat content is also an important trait index for high-yield cotton breeding. However, the traditional breeding work only improves t...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): C12Q1/6895C12N15/11
CPCC12Q1/6895C12Q2600/13C12Q2600/156
Inventor 李威杨代刚宋成祥裴小雨刘艳改贺昆仑张飞任中英孙宽马雄风周晓箭张文生
Owner INST OF COTTON RES CHINESE ACAD OF AGRI SCI
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