Scientia Agricultura Sinica ›› 2024, Vol. 57 ›› Issue (15): 2901-2913.doi: 10.3864/j.issn.0578-1752.2024.15.001

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

QTN Mining and Candidate Gene Screening of Upland Cotton (Gossypium hirsutum L.) Seed-Related Traits

BAI BingNan1(), QIAO Dan2, GE Qun2, LUAN YuJuan3, LIU XiaoFang3, LU QuanWei3, NIU Hao2, GONG JuWu2, GONG WanKui2, ELAMEER ELSAMMAN2, YAN HaoLiang2, LI JunWen2, LIU AiYing2, SHI YuZhen2, WANG HaiZe1(), YUAN YouLu2,4()   

  1. 1 College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163000, Heilongjiang
    2 Institute of Cotton Research, Chinese Academy of Agricultural Sciences/National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang 455000, Henan
    3 Anyang Institute of Technology, Anyang 455000, Henan
    4 School of Advanced Agricultural Sciences, Kashi University, Kashi 844000, Xinjiang
  • Received:2024-01-16 Accepted:2024-03-11 Online:2024-08-05 Published:2024-08-05
  • Contact: WANG HaiZe, YUAN YouLu

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Abstract:

【Objective】Exploring the genetic loci and related genes that control cottonseed size traits to lay a foundation for subsequent study on the molecular mechanism cottonseed size formation. 【Method】The upland cotton recombinant inbred line (RIL) population composed of 300 lines was used as the research material. Seven phenotypic traits including cottonseed index (SI), seed length-cutting acreage (SLA), seed length-cutting perimeter (SLP), seed length (SL), seed width (SW), length-width ratio (LWR) and seed roundness (SR) were evaluated in four environments. The RIL population was genotyped by liquid phase chip strategy. The high-quality single nucleotide polymorphism (SNP) markers and phenotypic data were subjected to perform genome-wide association study (GWAS), and quantitative trait nucleotides (QTNs) associated with cottonseed size-related traits were mined. The genetic effects of QTNs were analyzed to identify candidate genes. 【Result】Seven cottonseed size-related traits showed a continuous normal distribution in four environments, which expressed a sizable phenotypic variation. The coefficient of variation ranged from 1.82% to 10.70%. The influencing effect on trait formation were basically as genotype>environment>genotype × environment, indicating suitability for GWAS analysis of these results. Correlation analysis showed that the seed index was significantly correlated with SLA, SLP, SL and SW, and LWR was significantly correlated with SR, indicating the possible existence of pleiotropic loci. GWAS was performed using the 3VmrMLM model, and a total of 47 QTNs were associated with these seven traits. A total of 11 QTNs were associated on chromosome A07, of which three physical loci in the region of 71.99-72.87 Mb, A07:71993462, A07:72067994 and A07:72198802 were very close and simultaneously associated with SI, SLA, SLP, SL and SW in four environments. The average value of R2 between markers was>0.8 (P<0.001), showing a large linkage disequilibrium. Genetic effect analysis showed that there were two haplotypes in this region. Among these cottonseed size relating traits, haplotype Ⅱ and haplotype I were significantly different, indicating that these loci directly affected cottonseed size traits and could be used for molecular marker-assisted selection. The expression patterns of the genes in the interval were analyzed using TM-1 transcriptome data. The results revealed that Gh_A07G1767 was preferentially expressed and Gh_A07G1766 specifically expressed at the stage of cottonseed development. These results speculated that these genes may play an important role in the growth and development of cottonseed.【Conclusion】47 QTNs were identified, and two candidate genes related to cottonseed development were screened.

Key words: cotton, cottonseed, genome-wide association analysis, quantitative trait nucleotides, candidate genes

Table 1

Genetic variation of seed related traits in cotton population"

性状
Trait		 环境
Environment		 亲本Parents 重组自交系RIL
C60 ZR 范围
Range		 均值±标准差
Mean±SD		 变异系数
CV (%)		 偏度
Skewness		 峰度
Kurtosis
籽指SI (g) 20AY 9.95 9.35 8.45-15.35 11.06±1.16 10.44 0.46 0.21
21AY 12.30 12.30 9.55-16.70 12.60±1.30 10.28 0.28 -0.21
20WX 11.83 10.10 8.05-15.15 10.66±1.14 10.70 0.66 0.50
21WX 10.18 9.83 7.75-14.58 10.20±1.08 10.57 0.60 0.52
BLUE 9.01-15.68 11.39±1.12 9.88 0.49 0.18
面积SLA (mm²) 20AY 26.58 26.72 23.85-37.26 29.10±2.22 7.61 0.56 0.29
21AY 30.56 31.10 27.21-40.42 32.97±2.67 8.11 0.37 -0.29
20WX 29.75 27.95 24.83-38.83 29.52±2.26 7.65 0.66 0.69
21WX 26.90 26.92 23.31-35.81 28.77±2.22 7.72 0.53 0.06
BLUE 25.36-37.66 29.98±2.16 7.20 0.56 0.11
周长SLP (mm) 20AY 21.13 21.39 20.05-25.40 22.14±0.91 4.13 0.54 0.33
21AY 22.88 22.77 21.36-26.70 23.39±1.02 4.38 0.43 -0.09
20WX 22.35 21.76 20.43-25.90 22.44±0.94 4.21 0.60 0.49
21WX 21.13 21.40 19.47-25.10 21.93±0.94 4.28 0.51 0.23
BLUE 20.60-25.51 22.47±0.90 3.99 0.58 0.24
长度SL (mm) 20AY 8.28 8.28 7.70-9.85 8.56±0.37 4.35 0.54 0.35
21AY 8.85 8.89 8.06-10.49 9.01±0.42 4.68 0.43 0.15
20WX 8.61 8.49 7.80-10.15 8.58±0.40 4.66 0.60 0.62
21WX 8.18 8.31 7.45-9.86 8.46±0.40 4.68 0.51 0.38
BLUE 7.87-10.01 8.67±0.37 4.29 0.57 0.37
宽度SW (mm) 20AY 4.39 4.42 4.15-5.19 4.64±0.18 3.96 0.27 -0.21
21AY 4.73 4.78 4.43-5.56 5.01±0.22 4.34 0.06 -0.26
20WX 4.74 4.55 4.31-5.25 4.73±0.18 3.89 0.21 -0.28
21WX 4.49 4.45 4.10-5.19 4.65±0.18 3.88 0.20 -0.07
BLUE 4.26-5.25 4.74±0.17 3.67 0.21 -0.20
长宽比LWR 20AY 1.89 1.88 1.68-2.05 1.86±0.06 3.40 0.17 0.18
21AY 1.88 1.87 1.60-2.04 1.81±0.07 3.93 0.04 0.14
20WX 1.82 1.87 1.62-2.02 1.82±0.07 3.98 -0.01 -0.17
21WX 1.83 1.88 1.66-2.05 1.83±0.07 3.82 0.18 -0.07
BLUE 1.66-2.03 1.83±0.06 3.49 0.11 0.02
圆度SR 20AY 0.75 0.73 0.70-0.78 0.74±0.01 1.82 -0.27 -0.16
21AY 0.73 0.75 0.70-0.80 0.76±0.01 1.97 -0.10 0.12
20WX 0.92 0.74 0.65-0.78 0.74±0.02 2.63 -0.63 1.60
21WX 0.82 0.74 0.71-0.79 0.75±0.07 2.05 -0.18 -0.13
BLUE 0.71-0.78 0.75±0.01 1.74 -0.17 0.01

Fig. 1

Statistical analysis of cottonseed related traits in RIL population a: Seed related traits acquisition; b: Principal component analysis of seed related traits; c-i: Histogram of seed related traits of cotton varieties"

Table 2

Analysis of variance of kernel size-related traits in RIL populations"

变异来源
Source of variance		 基因型 Genotype 环境 Environment 基因型×环境 Genotype×Environment 误差平方和占比
Percentage of
squared error (%)
F值
F value		 百分比Percentage (%) P F值
F value		 百分比Percentage (%) P F值
F value		 百分比Percentage (%) P
籽指SI 15.74 46.53 <0.001 2180.02 37.95 <0.001 1.04 7.51 0.707 7.22
面积SLA 19.23 49.86 <0.001 1156.58 30.09 <0.001 1.12 8.70 0.036 10.28
周长SLP 23.90 58.95 <0.001 918.10 22.72 <0.001 1.09 8.07 0.082 9.78
长度SL 22.23 60.40 <0.001 694.81 18.94 <0.001 1.02 8.35 0.351 10.78
宽度SW 18.67 46.49 <0.001 1350.34 33.73 <0.001 1.28 9.56 <0.001 9.88
长宽比LWR 20.55 68.54 <0.001 155.23 5.19 <0.001 1.19 11.86 0.003 13.24
圆度SR 8.66 45.02 <0.001 232.47 12.12 <0.001 1.21 18.87 0.001 21.05

Fig. 2

Correlation analysis of cottonseed traits in RIL population"

Fig. 3

Mapping of population SNP genetic data a-b: Distribution of SNPs among 26 chromosomes; c: LD decay map of GWAS population; d: Principal component analysis of group structure"

Fig. 4

Associated SNPs and haplotypes on chromosome A07 for cotton seed related traits a: LD analysis of chromosome A07; b: Haplotypes of associated SNPs; c-i: Different related traits between haplotypes"

Fig. 5

Expressions of candidate genes associated to the adjacent developmental stages in cotton ovule"

Table 3

Candidate genes related to the seed size and shape in cotton"

候选基因
Candidate gene		 基因注释
Gene annotation		 表达量增加的时期（胚珠）
Stage with increasing expression (ovule)
Gh_A07G1760 CASP样蛋白5C2 CASP-like protein 5C2 开花后35 d 35 DPA
Gh_A07G1761 NA 开花后1 d 1 DPA
Gh_A07G1762 NA 开花后20 d 20 DPA
Gh_A07G1763 NA 开花后0 d 0 DPA
Gh_A07G1764 NA 开花后3 d 3 DPA
Gh_A07G1765 NA 开花后10 d 10 DPA
Gh_A07G1766 MYB家族转录因子APL MYB family transcription factor APL 开花后20 d 20 DPA
Gh_A07G1767 9次跨膜超家族蛋白成员 Transmembrane 9 superfamily member 全期Whole stage
Gh_A07G1768 NA 全期Whole stage
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