Genome-wide Association Study of Agronomic and Yield Traits in a Worldwide Collection of Peanut (Arachis hypogaea) Germplasm

doi:10.11983/CBB14144

Abstract

Abstract: Association analysis of yield-related traits and simple sequence repeat (SSR) loci distributed randomly in the peanut genome could contribute to marker-assisted selection breeding by the detection of elite alleles and the interaction of the gene region associated with high yield traits. We performed genome-wide association analysis with the mixed linear model (Q+K) by scanning 166 peanut germplasm with selected 64 SSR markers. In all, 166 peanut germplasm could be assigned to 7 subpopulations by population structure and cluster analysis, with results from both methods similar. The morphological characteristics and geographic origin of germplasm were consistent within model-based clusters. From 2011 to 2013, the number of detected SSR markers significantly associated with 6 yield-related traits was 20, 33 and 26 respectively; 13 markers (P<0.05) were detected repeatedly over 2 years. The mean rate of phenotypic explanation of SSR loci associated with traits was 0.067 3 (range 0.011-0.348 1). In total, 590 alleles were detected, with a mean of 12.29 alleles per SSR loci. Among all the trait-related markers, TC1A02 (P<0.001) had the highest rate of phenotypic explanation and contained 21 alleles, which was associated with the trait of pod number per plant. Among the SSR loci associated with the main effective factors of yield, the elite alleles with a high positive effect that could be used in marker-assisted selection of yield improvement were TC1A02-C560 (+40.926 1), TC1A02-C470 (+41.588 5), pPGPseq2E6-B473 (+63.953 4) associated with 100-pod weight, TC1A02-C500 (+7.374 4) associated with pod number per plant and GM1843-E157 (+4.316 6) associated with full pod number per plant.

Mei Yan, Xinyou Zhang, Suoyi Han, Bingyan Huang, Wenzhao Dong, Hua Liu, Ziqi Sun. Genome-wide Association Study of Agronomic and Yield Traits in a Worldwide Collection of Peanut (Arachis hypogaea) Germplasm[J]. Chinese Bulletin of Botany, 2015, 50(4): 460-472.

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URL: https://www.chinbullbotany.com/EN/10.11983/CBB14144

https://www.chinbullbotany.com/EN/Y2015/V50/I4/460

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SSR locus	Linkage	Position	Allele No.	Gene diversity	PIC	SSR locus	Linkage	Position	Allele No.	Gene diversity	PIC
ARS335	LK1	0	9	0.824	0.801	pPGPseq5D5	LK14	0	26	0.911	0.904
ARS303	LK1	2	14	0.789	0.763	TC2G05	LK14	16	10	0.858	0.842
ARS166	LK1	6.3	11	0.835	0.815	TC6E01	LK14	68.8	28	0.944	0.941
ARS535	LK1	21.7	5	0.716	0.681	TC2B09	LK14	112.1	7	0.713	0.666
ARS415	LK1	24.4	8	0.833	0.811	GM28	LK14	158.8	10	0.765	0.733
GC-94	LK1	28.8	14	0.758	0.737	ARS203	LK15	30.2	17	0.812	0.788
GC-104	LK1	44.4	15	0.868	0.853	TC1A02	LK15	52.2	21	0.764	0.734
pPGSseq19G7	LK2	0	8	0.84	0.82	PM54	LK16	0	10	0.796	0.765
PM81	LK2	10.6	6	0.36	0.338	pPGPseq3E10	LK17	0	9	0.814	0.787
ARS392	LK2	51.6	10	0.815	0.788	pPGPseq4H11	LK17	13.4	15	0.731	0.697
ARS251	LK2	60.3	12	0.862	0.848	PMc588	-		6	0.635	0.569
ARS180	LK2	73	12	0.874	0.86	pPGSseq15D3	-		10	0.724	0.688
GM553	LK3	0	12	0.847	0.829	pPGSseq18G1	-		6	0.637	0.571
pPGSseq16F1	LK3	36.3	6	0.799	0.768	pPGPseq2E6	-		19	0.812	0.792
ARS173	LK4	0	16	0.844	0.825	pPGPseq2D12B	-		7	0.711	0.678
ARS298	LK4	0.891	19	0.874	0.861	PM137	-		13	0.809	0.786
GM1843	LK4	3.464	9	0.778	0.744	PM377	-		13	0.798	0.775
GM401	LK4	51.1	9	0.744	0.699	TC4G02	-		20	0.837	0.823
ARS313	LK6	25.4	5	0.448	0.4	GM529	-		9	0.744	0.704
EM-87	LK7	4.8	18	0.829	0.808	TC1G04	-		10	0.674	0.626
ARS376	LK7	25.2	13	0.839	0.82	TC2E05	-		13	0.719	0.675
pPGSseq17E3	LK7	49.9	6	0.705	0.661	TC3G05	-		11	0.697	0.646
ARS644	LK7	62.6	4	0.534	0.449	TC4G02	-		11	0.823	0.801
pPGPseq1B9	LK8	0	11	0.816	0.791	RN26G09	-		14	0.89	0.879
ARS545	LK9	33.9	15	0.867	0.852	RN34A10	-		9	0.69	0.635
ARS127	LK10	33.3	3	0.549	0.451	ARS98	-		10	0.818	0.794
ARS357	LK11	6.5	7	0.823	0.799	ARS108	-		14	0.869	0.856
PM436	LK12	41.7	9	0.822	0.8	ARS124	-		7	0.75	0.706
pPGSseq14H6	LK12	47.7	11	0.829	0.808	ARS318	-		13	0.88	0.868
pPGSseq15C12	LK13	0	17	0.855	0.841	ARS338	-		16	0.859	0.844
pPGSseq17F6	LK13	50.8	21	0.917	0.911	ARS369	-		9	0.615	0.567
						ARS606	-		10	0.808	0.78
						GM384	-		6	0.751	0.711
Mean			11.6	0.777	0.748

SSR locus	Linkage	Position	Allele No.	Gene diversity	PIC	SSR locus	Linkage	Position	Allele No.	Gene diversity	PIC
ARS335	LK1	0	9	0.824	0.801	pPGPseq5D5	LK14	0	26	0.911	0.904
ARS303	LK1	2	14	0.789	0.763	TC2G05	LK14	16	10	0.858	0.842
ARS166	LK1	6.3	11	0.835	0.815	TC6E01	LK14	68.8	28	0.944	0.941
ARS535	LK1	21.7	5	0.716	0.681	TC2B09	LK14	112.1	7	0.713	0.666
ARS415	LK1	24.4	8	0.833	0.811	GM28	LK14	158.8	10	0.765	0.733
GC-94	LK1	28.8	14	0.758	0.737	ARS203	LK15	30.2	17	0.812	0.788
GC-104	LK1	44.4	15	0.868	0.853	TC1A02	LK15	52.2	21	0.764	0.734
pPGSseq19G7	LK2	0	8	0.84	0.82	PM54	LK16	0	10	0.796	0.765
PM81	LK2	10.6	6	0.36	0.338	pPGPseq3E10	LK17	0	9	0.814	0.787
ARS392	LK2	51.6	10	0.815	0.788	pPGPseq4H11	LK17	13.4	15	0.731	0.697
ARS251	LK2	60.3	12	0.862	0.848	PMc588	-		6	0.635	0.569
ARS180	LK2	73	12	0.874	0.86	pPGSseq15D3	-		10	0.724	0.688
GM553	LK3	0	12	0.847	0.829	pPGSseq18G1	-		6	0.637	0.571
pPGSseq16F1	LK3	36.3	6	0.799	0.768	pPGPseq2E6	-		19	0.812	0.792
ARS173	LK4	0	16	0.844	0.825	pPGPseq2D12B	-		7	0.711	0.678
ARS298	LK4	0.891	19	0.874	0.861	PM137	-		13	0.809	0.786
GM1843	LK4	3.464	9	0.778	0.744	PM377	-		13	0.798	0.775
GM401	LK4	51.1	9	0.744	0.699	TC4G02	-		20	0.837	0.823
ARS313	LK6	25.4	5	0.448	0.4	GM529	-		9	0.744	0.704
EM-87	LK7	4.8	18	0.829	0.808	TC1G04	-		10	0.674	0.626
ARS376	LK7	25.2	13	0.839	0.82	TC2E05	-		13	0.719	0.675
pPGSseq17E3	LK7	49.9	6	0.705	0.661	TC3G05	-		11	0.697	0.646
ARS644	LK7	62.6	4	0.534	0.449	TC4G02	-		11	0.823	0.801
pPGPseq1B9	LK8	0	11	0.816	0.791	RN26G09	-		14	0.89	0.879
ARS545	LK9	33.9	15	0.867	0.852	RN34A10	-		9	0.69	0.635
ARS127	LK10	33.3	3	0.549	0.451	ARS98	-		10	0.818	0.794
ARS357	LK11	6.5	7	0.823	0.799	ARS108	-		14	0.869	0.856
PM436	LK12	41.7	9	0.822	0.8	ARS124	-		7	0.75	0.706
pPGSseq14H6	LK12	47.7	11	0.829	0.808	ARS318	-		13	0.88	0.868
pPGSseq15C12	LK13	0	17	0.855	0.841	ARS338	-		16	0.859	0.844
pPGSseq17F6	LK13	50.8	21	0.917	0.911	ARS369	-		9	0.615	0.567
						ARS606	-		10	0.808	0.78
						GM384	-		6	0.751	0.711
Mean			11.6	0.777	0.748

Geographic eco-type	Structure							Total	χ²test
Geographic eco-type	I	II	III	IV	V	VI	VII	Total	χ²test
Southeast of China	1		25	18	2			46
Huang River region of China	17	23	6	2	7		1	56	χ²=166^**
Yangtzi River region of China	11	6	4	3	6		1	31	P<0.000 1
Yunnan and Guizhou Plateau	1			2				3
World wide origin	1			8		13	8	30	χ²_{0.01, 24}= 42.98
Total	31	29	35	33	15	13	10	166

Geographic eco-type	Structure							Total	χ²test
Geographic eco-type	I	II	III	IV	V	VI	VII	Total	χ²test
Southeast of China	1		25	18	2			46
Huang River region of China	17	23	6	2	7		1	56	χ²=166^**
Yangtzi River region of China	11	6	4	3	6		1	31	P<0.000 1
Yunnan and Guizhou Plateau	1			2				3
World wide origin	1			8		13	8	30	χ²_{0.01, 24}= 42.98
Total	31	29	35	33	15	13	10	166

Trait	I	II	III	IV	V	VI	VII
1	45.21±1.92	46.93±0.83	48.82±1.25	55.92±1.97	45.58±1.59	79.51±2.81	53.80±2.89
2	53.77±1.24	55.93±1.18	58.96±1.42	66.95±2.23	54.14±2.06	95.07±3.64	70.63±3.07
3	11.37±0.50	11.55±0.60	10.31±0.32	10.33±0.36	10.74±0.66	10.38±0.88	19.02±1.40
4	8.99±0.16	8.96±0.24	7.29±0.15	7.37±0.20	8.57±0.40	6.88±0.32	11.1±0.67
5	28.64±0.79	27.91±0.61	21.20±0.92	20.80±1.01	27.3±1.41	15.74±1.12	19.45±1.85
6	23.71±0.52	22.51±0.48	20.08±0.50	21.68±0.75	24±0.83	17.89±0.89	22.56±0.86
7	16.8±0.36	15.3±0.46	14.6±0.41	16.53±0.54	16.01±0.69	12.27±0.70	13.26±0.76
8	176.58±6.05	176.93±3.93	139.16±3.47	135.32±6.46	172.81±6.34	120.17±6.99	123.78±11.54
9	75.47±2.33	76.93±1.59	54.92±1.54	53.59±2.45	69.60±2.78	39.85±2.34	55.05±3.82
10	0.51±0.01	0.51±0.01	0.48±0.01	0.49±0.01	0.51±0.01	0.49±0.01	0.46±0.02