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

中国农业科学 ›› 2024, Vol. 57 ›› Issue (15): 2901-2913.doi: 10.3864/j.issn.0578-1752.2024.15.001

• 作物遗传育种·种质资源·分子遗传学 • 上一篇下一篇

陆地棉棉籽相关性状的QTN挖掘及候选基因筛选

白冰楠¹(), 乔丹², 葛群², 栾玉娟³, 刘小芳³, 卢全伟³, 牛皓², 龚举武², 巩万奎², ELAMEER ELSAMMAN², 闫浩亮², 李俊文², 刘爱英², 石玉真², 王海泽¹(), 袁有禄²^,⁴()

¹ 黑龙江八一农垦大学农学院，黑龙江大庆 163000
² 中国农业科学院棉花研究所/棉花生物育种与综合利用国家重点实验室，河南安阳 455000
³ 安阳工学院，河南安阳 455000
⁴ 喀什大学现代农学院，新疆喀什 844000

收稿日期:2024-01-16 接受日期:2024-03-11 出版日期:2024-08-05 发布日期:2024-08-05
通信作者:
王海泽，E-mail：290832536@qq.com
袁有禄，E-mail：yuanyoulu@caas.com
联系方式: 白冰楠，E-mail：1791152216@qq.com
基金资助:
国家自然科学基金(32070560); 农业科技创新工程(CAAS-ASTIP-2016-ICR); 新疆维吾尔自治区自然科学基金(2021D01B114); 新疆维吾尔自治区重大科技专项计划(2021A02001-3)

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 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 Published:2024-08-05 Online:2024-08-05

摘要/Abstract

摘要：

【目的】挖掘控制棉籽大小性状相关的遗传位点和相关基因，为研究棉籽大小性状形成的分子机理奠定基础。【方法】以陆地棉构建的含有300个家系的重组自交系（recombinant inbred line，RIL）群体为研究对象，对4个环境的棉籽籽指、面积、周长、长度、宽度、长宽比、圆度7个性状进行表型鉴定，利用液相芯片对RIL群体进行基因分型，得到的高质量单核苷酸多态性（single nucleotide polymorphism，SNP）位点和表型数据进行全基因组关联分析（genome-wide association study，GWAS），挖掘控制棉籽大小相关性状的数量性状遗传位点（quantitative trait nucleotides，QTN），对数量性状遗传位点进行遗传效应分析，筛选候选基因。【结果】7个棉籽大小相关性状在4个环境中均表现为连续正态分布，且具有明显的表型变异，变异系数的范围为1.82%-10.70%，性状的影响基本表现为基因型>环境>基因型×环境，适用于GWAS分析。相关分析表明，籽指与面积、周长、长度、宽度显著相关，长宽比与圆度显著相关，表明可能存在一因多效位点。利用3VmrMLM模型进行全基因组关联分析，共定位到47个与棉籽大小性状相关的数量遗传位点。A07染色体上共定位到11个数量遗传位点，其中，A07：71993462、A07：72067994和A07：72198802的位点物理位置接近，在4个环境中稳定存在，与棉籽籽指、面积、周长、长度和宽度关。这3个数量遗传位点位于A07染色体71.99-72.87 Mb区间，标记间R²的平均值>0.8（P<0.001），呈现较大的连锁不平衡。遗传效应分析发现，该区段存在2种单倍型，在棉籽大小的相关性状中，单倍型Ⅱ与单倍型Ⅰ差异性显著，表明该位点直接影响棉籽大小性状，可用于分子标记辅助选择。利用TM-1转录组数据对区间内的基因进行表达模式分析，发现Gh_A07G1767在棉籽发育阶段优势表达，Gh_A07G1766在棉籽发育阶段特异性表达，推测其在棉籽生长发育过程中发挥重要的作用。【结论】鉴定了47个QTN，筛选了2个与棉籽发育相关的候选基因。

关键词: 棉花, 棉籽, 全基因组关联分析, 数量性状遗传位点, 候选基因

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

白冰楠, 乔丹, 葛群, 栾玉娟, 刘小芳, 卢全伟, 牛皓, 龚举武, 巩万奎, ELAMEER ELSAMMAN, 闫浩亮, 李俊文, 刘爱英, 石玉真, 王海泽, 袁有禄. 陆地棉棉籽相关性状的QTN挖掘及候选基因筛选[J]. 中国农业科学, 2024, 57(15): 2901-2913.

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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图/表 8

表1

群体棉籽相关性状遗传变异"

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

表1

图1

表2

图2

图3

图4

图5

表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

陆地棉棉籽相关性状的QTN挖掘及候选基因筛选

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

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