CN107201403B - Cotton fiber length related QTL and application thereof - Google Patents

Cotton fiber length related QTL and application thereof Download PDF

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CN107201403B
CN107201403B CN201710434758.XA CN201710434758A CN107201403B CN 107201403 B CN107201403 B CN 107201403B CN 201710434758 A CN201710434758 A CN 201710434758A CN 107201403 B CN107201403 B CN 107201403B
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qtl
fiber length
cotton
quhm
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汪保华
庄智敏
张咪
黄芳
高新岩
周水娟
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Abstract

The invention relates to the field of plant genetics, in particular to a cotton fiber length-related QTL and application thereof. The cotton fiber length-related QTL qUHM-1-1 is located on chromosome 1, and the adjacent marker is BNL3580-BNL1667, the cotton fiber length-related QTL qUHM-22-1 is located on chromosome 22, and the adjacent marker is NAU3093-CICR 345. The fiber length related QTL of the invention is detected in two environments and has the stability independent of the environment.

Description

Cotton fiber length related QTL and application thereof
Technical Field
The invention relates to the field of plant genetics, in particular to a cotton fiber length-related QTL and application thereof.
Background
Quantitative Trait Loci (QTL) are regions on a chromosome that affect Quantitative traits, and a Quantitative trait is often affected by multiple Quantitative Trait Loci (QTLs) distributed at different locations in the genome. Up to now, QTL mapping has been performed by constructing segregating populations based on parental crosses and correlation analysis. However, current low density genetic maps and temporal segregation populations make the precision and stability of the QTL detected less than ideal, and there are few cotton fiber quality-related QTLs that could be applied to molecular breeding of cotton
Disclosure of Invention
The invention aims to provide a cotton fiber length-related QTL.
Still another object of the present invention is the specific SSR primer for cotton fiber length-related QTL described above.
The cotton fiber length related QTL qUHM-1-1 according to the invention is located on chromosome 1 and is flanked by the markers BNL3580-BNL 1667.
The cotton fiber length related QTL qUHM-22-1 according to the invention is located on chromosome 22 and is flanked by the markers NAU3093-CICR 345.
The sequence of the specific SSR primer of the cotton fiber length related QTL qUHM-1-1 is as follows:
BNL3580F：5'CTTGTTTACATTCCCTTCTTTATACC 3'；
BNL3580R:5'CAAAGGCGAACTCTTCCAAA 3'；
BNL1667F:5'AGGTGCTTCAGGCATGATTC 3'；
BNL1667R:5'CCCTCACACCTAAACCCAAA 3'。
the sequence of the specific SSR primer of the cotton fiber length related QTL qUHM-22-1 is as follows:
NAU3093F：5'GATGGGCAGAGGCTACTTTG 3'
NAU3093R：5'GATGGGCAGAGGCTACTTTG 3'
CICR0345-F：5'GATGGGCAGAGGCTACTTTG 3'
CICR0345-R：5'GATGGGCAGAGGCTACTTTG 3'。
according to the specific embodiment of the invention, the cotton is upland PD94042 (P)1) Is the receptor parent and is made of brown cotton (G. mustelinum) (P)2) Crossing with upland cotton PD94042 (P)1) Backcross the third generation of parent recurrent, then construct backcross high generation group, breed a set of import line covering cotton whole genome from it, total 65 materials, carry on backcross high generation QTL analysis (AB-QTL). The analysis of the import group data comprises the following steps:
(1) genotype data statistics
Recording the types of parent and progeny SSR markers: with the parent (P)1) The same homozygous banding pattern is designated "1" as the parent (P)2) The same homozygous band pattern was designated "2", the heterozygous band pattern of both parents was designated "3", the fuzzy or missing data was designated "0"; when the parent is (P)1) Being recessive, the parent (P)2) When dominant, P1The tape type is marked as "1", P2、F1The band pattern is marked as "4", when the parent is (P)1) Being dominant, the parent (P)2) When recessive, P2The tape type is denoted as "2", P1、F1The tape pattern is denoted as "5".
(2) Statistics of phenotypic data
Statistical analysis such as average value, range, variation coefficient and skewness is carried out on the three-year fiber quality phenotype data, and a histogram is prepared from the phenotype data of the imported system.
(3) Construction of genetic map and QTL location
And (3) integrating the genotype data of the introgression line population, comparing the sequence corresponding to each molecular marker with a tetraploid upland cotton genome database to obtain the genome position of each molecular marker, and analyzing the linkage relation among the markers by taking the genome position as reference information to construct the genetic linkage map of the molecular markers. Combining the genotype data and the phenotype data of the fiber quality, carrying out fine positioning on the fiber quality QTL and analyzing the result, detecting that the lowest LOD value of the QTL is 2.0, and finally, carrying out linkage mapping or chromosome position on the target QTL.
The fiber length related QTL qUHM-1-1 and qUHM-22-1 are respectively positioned on chromosome 1 and chromosome 22 (as shown in figure 2), the contribution rate is high, and the favorable genes are all from the yellow brown cotton.
Compared with the existing fiber length stable QTL, the invention provides the fiber length related QTL respectively located on chromosome 1 and chromosome 22 of cotton, which is detected in two environments and has environment-independent stability.
Drawings
FIG. 1 shows the strength of the fulvic introduction fiber;
FIG. 2 shows genetic maps of chromosomes 1 and 22 constructed based on the introduction line of Phaseolus angularis;
FIG. 3 shows two stable major QTLs for fiber length, where group A is fiber length QTL qUHM-1-1 and group B is fiber length QTL qUHM-22-1.
FIG. 4 shows near isogenic lines selected based on fiber length QTL qUHM-1-1 and qUHM-22-1, light gray for pure and upland cotton genotypes and black for yellow-brown cotton introgression.
Detailed Description
Example 1
With upland cotton PD94042 (P)1) As acceptor parent, takes the yellow brownCotton (g. mustelinum) (P)2) Crossing with upland cotton PD94042 (P)1) Backcross the third generation of the recurrent parent, construct backcross high-generation population by selfing the third generation, breed a set of introgression lines covering the whole genome of the cotton from the population, count 65 materials, and carry out backcross high-generation QTL analysis. Extracting DNA of cotton leaves and carrying out SSR molecular marking. And (3) screening out primers with polymorphism between PD94042 and the fulvic cotton, and scanning and QTL (quantitative trait locus) analysis are carried out on fulvic cotton introgression line groups.
1. Introductive population data analysis
(1) Genotype data statistics
Recording the types of parent and progeny SSR markers: with the parent (P)1) The same homozygous banding pattern is designated "1" as the parent (P)2) The same homozygous band pattern was designated "2", the heterozygous band pattern of both parents was designated "3", the fuzzy or missing data was designated "0"; when the parent is (P)1) Being recessive, the parent (P)2) When dominant, P1The tape type is marked as "1", P2、F1The band pattern is marked as "4", when the parent is (P)1) Being dominant, the parent (P)2) When recessive, P2The tape type is denoted as "2", P1、F1The tape pattern is denoted as "5".
(2) Statistics of phenotypic data
Statistical analysis such as average value, range, variation coefficient and skewness is carried out on the three-year fiber quality phenotype data, and a histogram is prepared from the phenotype data of the imported system.
(3) Construction of genetic map and QTL location
And (3) integrating the genotype data of the introgression line population, comparing the sequence corresponding to each molecular marker with a tetraploid upland cotton genome database to obtain the genome position of each molecular marker, and analyzing the linkage relation among the markers by taking the genome position as reference information to construct the genetic linkage map of the molecular markers. Combining the genotype data and the phenotype data of the fiber quality, carrying out fine positioning on the fiber quality QTL and analyzing the result, detecting that the lowest LOD value of the QTL is 2.0, and finally, carrying out linkage mapping or chromosome position on the target QTL.
A total of 28 fiber length QTLs were detected covering a total of 18 chromosomes. According to the additive effect, the favorable alleles of 6 QTLs are from upland cotton PD94042, and the favorable alleles of the rest 22 QTLs are from yellow brown cotton. Most of the fiber length QTL are detected in only one environment, but 3 QTL are detected in two consecutive years, and the marker intervals of qUHM-1-1 and qUHM-22-1 are the same (figure 3), which shows that the QTL have the stability independent of the environment.
The fiber length related QTL qUHM-1-1 and qUHM-22-1 are respectively positioned on chromosome 1 and chromosome 22 (as shown in figure 2), the contribution rate is high, and the favorable genes are all from the yellow brown cotton.
TABLE 2.6 fiber Length QTL
Figure BDA0001318336520000041
Note: y1 denotes the first year; y2 denotes the second year, both representing different environments (the same applies hereinafter)
Based on the fiber length major QTL on chromosome 1: qUHM-1-1, a set of near isogenic lines (figure 4) is established, which comprises 4 excellent introduction lines of IL6, IL9, IL15 and IL17, all or most of the introduction lines are yellow-brown cotton introgression genes between lateral adjacent marker sites BNL3580-BNL1667, and the rest parts are almost upland cotton genes.
And based on the fiber length major QTL on chromosome 22: the near isogenic line set up by qUHM-22-1 (FIG. 4) also contains 4 excellent introgression lines, IL6, IL9, IL11 and IL 17. As can be seen, half of the genes for introgression into Phaseolus fulvus are located between the adjacent markers NAU3093-CICR345 of qUHM-22-1, and not only does this result, but there is a fragment of introgression into Phaseolus fulvus from IL9, IL11, and IL17 around the marker NAU 5046.
In conclusion, the 5 introduced lines have the genes of the fulvous cotton around the major QTL of the fiber length, which shows that the genes are related to the beneficial genes of the fiber length.
The invention obtains two major QTLs of fiber length: qUHM-1-1, qUHM-22-1, and integrating the phenotypic data of fiber length to obtain 5 introgression line varieties with the fiber length between 32 and 34 mm: IL6, IL9, IL11, IL15, IL 17. Based on the fiber length major QTL on chromosome 1: qUHM-1-1, a set of near isogenic lines (figure 4) is established, which comprises 4 excellent introduction lines of IL6, IL9, IL15 and IL17, all or most of the introduction lines are yellow-brown cotton introgression genes between lateral adjacent marker sites BNL3580-BNL1667, and the rest parts are almost upland cotton genes. And based on the fiber length major QTL on chromosome 22: the near isogenic line set up by qUHM-22-1 (FIG. 4) also contains 4 excellent introgression lines, IL6, IL9, IL11 and IL 17. As can be seen, half of the genes for introgression into Phaseolus fulvus are located between the adjacent markers NAU3093-CICR345 of qUHM-22-1, and not only does this result, but there is a fragment of introgression into Phaseolus fulvus from IL9, IL11, and IL17 around the marker NAU 5046. In conclusion, the 5 introduced lines all have the genes of the fulvous cotton around the major QTL of the fiber length, which shows that the genes can be greatly related to the beneficial genes of the fiber length. By combining the introgression conditions of the fulvic acid cotton genes on the chromosomes 1 and 22, the introduction lines IL6, IL9 and IL17 have fulvic acid cotton genes related to fiber length on the two chromosomes and can be used as a preferential selection material for subsequent research.
Example 2
With upland cotton PD94042 (P)1) Is the receptor parent and is made of brown cotton (G. mustelinum) (P)2) Crossing with upland cotton PD94042 (P)1) Backcross the third generation of parent recurrent, then self-cross the third generation to construct backcross high generation population, breed a set of introgression lines covering the whole genome of cotton from the population, and carry out backcross high generation QTL analysis. Extracting DNA of cotton leaves, and performing SSR molecular markers by using primers shown in the following table, wherein the detection result of the SSR molecules is consistent with the genotype data statistics in example 1, which indicates that the primers shown in the table 1 are specific SSR primers of cotton fiber length-related QTL.
TABLE 1 specific SSR primers
Primer name Primer sequence ((5'-3'))
BNL3580F CTTGTTTACATTCCCTTCTTTATACC
BNL3580R CAAAGGCGAACTCTTCCAAA
BNL1667F AGGTGCTTCAGGCATGATTC
BNL1667R CCCTCACACCTAAACCCAAA
NAU3093F GATGGGCAGAGGCTACTTTG
NAU3093R AGCACAGGAGCAAAGGAAAA
CICR0345-F CTAAGACCGAGTGGCTTGAT
CICR0345-R AGCCAAATCCAGTAAACAGC
<110> university of southeast Tong
<120> cotton fiber length related QTL and application thereof
<160>8
<210>1
<211>26
<212>DNA
<213> Artificial sequence
<400>1
cttgtttaca ttcccttctt tatacc 26
<210>2
<211>20
<212>DNA
<213> Artificial sequence
<400>2
caaaggcgaa ctcttccaaa 20
<210>3
<211>20
<212>DNA
<213> Artificial sequence
<400>3
aggtgcttca ggcatgattc 20
<210>4
<211>20
<212>DNA
<213> Artificial sequence
<400>4
ccctcacacc taaacccaaa 20
<210>5
<211>20
<212>DNA
<213> Artificial sequence
<400>5
gatgggcaga ggctactttg 20
<210>6
<211>20
<212>DNA
<213> Artificial sequence
<400>6
gatgggcaga ggctactttg 20
<210>7
<211>20
<212>DNA
<213> Artificial sequence
<400>7
gatgggcaga ggctactttg 20
<210>8
<211>20
<212>DNA
<213> Artificial sequence
<400>8
gatgggcaga ggctactttg 20

Claims (1)

1. Cotton QTLqUHM-1-1Use as cotton fiber length-related QTL, wherein the cotton QTL isqUHM-1-1The specific SSR primers are as follows:
BNL3580F：5' CTTGTTTACATTCCCTTCTTTATACC 3';
BNL3580R: 5' CAAAGGCGAACTCTTCCAAA 3';
BNL1667F: 5' AGGTGCTTCAGGCATGATTC 3 ';
BNL1667R: 5' CCCTCACACCTAAACCCAAA 3'。
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CN111793714A (en) * 2020-08-06 2020-10-20 南通大学 Yellow-brown cotton fiber length related QTL and application thereof
CN112011638A (en) * 2020-09-02 2020-12-01 南通大学 Yellow-brown cotton fiber fineness related QTL and application thereof
CN114634993B (en) * 2022-04-27 2023-03-14 南通大学 Transcriptome and proteome combined analysis-based cotton salt-tolerant gene discovery method and application thereof

Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN101613761A (en) * 2009-08-12 2009-12-30 中国农业科学院棉花研究所 The SSR mark chain with the cotton fiber strength major gene

Patent Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN101613761A (en) * 2009-08-12 2009-12-30 中国农业科学院棉花研究所 The SSR mark chain with the cotton fiber strength major gene

Non-Patent Citations (3)

* Cited by examiner, † Cited by third party
Title
Identification of QTL for Fiber Quality and Yield Traits Using Two Immortalized Backcross Populations in Upland Cotton;Hantao Wang等;《PLoS ONE》;20161201;第11卷(第12期);第1-14页 *
Molecular mapping of QTLs for fiber qualities in three diverse lines in Upland cotton using SSR markers;Xinlian Shen等;《Molecular Breeding》;20051231;第15卷;第169-181页 *
陆海杂交高代回交重组近交系纤维品质和产量分子标记研究;张科;《中国优秀硕士学位论文全文数据库》;20100715(第07期);第23页第2.1节，第25页第2.2.2节，第28页第2.2.4节 *

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