陆地棉棉籽相关性状的QTN挖掘及候选基因筛选

doi:10.3864/j.issn.0578-1752.2024.15.001

Abstract

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

BAI BingNan, QIAO Dan, GE Qun, LUAN YuJuan, LIU XiaoFang, LU QuanWei, NIU Hao, GONG JuWu, GONG WanKui, ELAMEER ELSAMMAN, YAN HaoLiang, LI JunWen, LIU AiYing, SHI YuZhen, WANG HaiZe, YUAN YouLu. QTN Mining and Candidate Gene Screening of Upland Cotton (Gossypium hirsutum L.) Seed-Related Traits[J].Scientia Agricultura Sinica, 2024, 57(15): 2901-2913.

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Figures/Tables 8

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
性状 Trait	环境 Environment	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

Table 1

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Table 2

Fig. 2

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Table 3

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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 (%)
变异来源 Source of variance	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	误差平方和占比 Percentage of squared error (%)
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

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

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

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