花生荚果产量相关性状QTL定位与候选基因分析

doi:10.3724/SP.J.1006.2025.44158

Abstract

Abstract:

Peanut (Arachis hypogaea L.) is an important economic and oilseed crop in China, with pod traits playing a critical role in determining yield. In this study, a recombinant inbred line (RIL) population derived from a cross between the large-pod local variety “Dongguan Banman (DB)” and the small-pod variety “ZLA” was used to construct a high-density genetic map with single nucleotide polymorphism (SNP) markers. This map was employed to identify quantitative trait loci (QTL) associated with pod traits across four distinct cultivation environments. A total of 30 QTLs were mapped to chromosomes A01, A03, A05, A06, A07, A08, B02, B04, B06, and B10, with logarithm of odds (LOD) values ranging from 4.04 to 34.17 and contribution rates from 3.10% to 33.52%. Among these, 13 major QTLs were associated with pod length, width, thickness, and 100-pod weight, showing LOD values between 4.41 and 34.17 and contribution rates between 11.21% and 33.52%. Notably, qPLA07 was consistently detected across all four environments, while qPWA08.1, qPWB02, and qPTB06 were stable in three environments. Additionally, 14 epistatic QTLs were identified, with LOD values ranging from 5.07 to 6.67 and phenotypic variation explained (PVE) from 4.21% to 21.84%. KEGG pathway enrichment analysis of genes within the QTL regions of qPWA08.1, qPWB02, and qPTB06 identified four candidate genes: Ahy_A08g039622, Ahy_B02g057642, Ahy_B06g085859, and Ahy_B06g085890, based on gene functional annotation and expression analysis across peanut tissues. These findings provide a theoretical foundation for identifying key genes regulating peanut pod yield and for developing molecular markers to facilitate breeding programs.

Key words: peanut, pod, QTL, candidate genes

LIN Wei-Jin, GUO Ze-Jia, LIU Hao, LI Hai-Fen, WANG Run-Feng, HUANG Lu, YU Qian-Xia, CHEN Xiao-Ping, HONG Yan-Bin, LI Shao-Xiong, LU Qing. QTL mapping and candidate gene analysis of peanut pod yield-related traits[J].Acta Agronomica Sinica, 2025, 51(4): 969-981.

Figures/Tables 10

Fig. 1

Table 1

Table 2

Fig. 2

Table 3

Results of QTL analysis of related traits of peanut pod"

性状 Trait	位点 QTL	环境 Environment	染色体 Chr.	标记区间 Marker interval	LOD	贡献率 PVE (%)	加性效应 Additive effect	置信区间 Confidence interval
荚果长 PL (mm)	qPLA01	E2	A01	A01_11204930-11352342	7.0403	15.2310	-1.8397	37.5-40.5
	qPLA05	E2	A05	A05_8652005-11538045	4.5490	11.2089	-1.5964	192.0-203.5
	qPLA06	E1	A06	A06_1765658-3081683	4.6951	8.7442	1.9602	0-8.5
	qPLA07	E1	A07	A07_166832022-166955022	14.6721	31.2684	3.7220	488.5-491.0
		E2	A07		9.1447	21.7858	2.2249	486.5-491.0
		E3	A07		5.9719	16.2443	2.4481	484.5-491.0
		E4	A07		6.3490	17.2817	2.1865	487.5-491.0
荚果宽 PW (mm)	qPWA03	E4	A03	A03_143317504-144635493	4.9992	9.3638	0.5257	354.0-363.0
	qPWA06	E4	A06	A06_115549348-115817873	4.4243	7.9380	0.4776	197.0-199.0
	qPWA08.1	E1	A08	A08_30048499-30366347	6.0062	15.6656	0.7732	64.5-65.5
		E2	A08		7.6455	21.6332	0.9226	65.5-67.5
		E4	A08		5.6550	10.5400	0.5522	65.5-67.5
	qPWA08.2	E3	A08	A08_37177561-37928646	6.1705	3.3958	0.7702	77.5-78.5
	qPWB02	E2	B02	B02_4887376-5205416 B02_5205416-6387357	6.0087	16.2445	0.8084	34.5-38.5
	qPWB02	E3	B02		5.8390	3.0950	0.7437	34.5-37.5
		E4	B02		6.6999	13.4146	0.6311	34.5-38.5
	qPWB06	E1	B06	B06_138639856-140196491	5.9124	15.4844	0.7643	48.5-49.5
	qPWB10	E3	B10	B10_33405033-32604657	34.1719	33.5202	-2.4344	63.5-64.5
荚果厚 PT (mm)	qPTA03	E4	A03	A03_143317504-144635493	4.1054	9.5411	0.4756	354-362.0
	qPTA08	E4	A08	A08_30048499-30366347	4.2747	9.9395	0.4815	64.5-65.5
	qPTA08	E1	A08	A08_30048499-30366347	8.2452	15.9256	0.8437	65.5-66.5
	qPTB02	E1	B02	B02_4887376-5205416	8.3107	15.8808	0.8525	34.5-37.5
	qPTB04	E1	B04	B04_127248538-126884743	4.9720	9.6182	0.7093	88.5-89.0
	qPTB06	E2	B06	B06_146907751-148783006	6.6930	18.5502	0.9310	70.5-77.0
		E3	B06		4.2572	14.1986	0.6975	70.5-77.0
		E4	B06		5.8566	15.7462	0.4526	71.5-77.0
百果重 HPW (g)	qHPWA03.1	E1	A03	A03_141234947-141092590	4.9493	14.1606	16.6366	339.0-342.0
	qHPWA03.2	E2	A03	A03_139238268-139848157	6.7751	12.7953	15.2542	321.0-325.0
	qHPWA06	E2	A06	A06_113190229-113520763	4.0418	7.0298	11.1996	185.0-192.0
	qHPWB10	E1	B10	B10_145433611-145968886	4.4101	11.7996	14.5291	174.0-184.0

Table 3

Fig. 3

Table 4

Fig. 4

Table 5

Fig. 5

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性状 Trait	环境 Environment	亲本 Parent		RIL群体 RIL population
		ZLA	东莞半蔓 Dongguan Banman	最大值 Max.	最小值 Min.	变异系数 CV (%)	标准差 SD	平均值 Mean	偏度 Skewness	峰度 Kurtosis
		荚果长 PL (mm)	E1	0.65	0.74^**	52.57	23.30	0.18	6.13	33.40	0.695	0.480
E2	0.58		0.68^**	42.09	22.16	0.14	4.35	32.21	-0.046	-0.416
E3	0.63		0.69^**	53.04	23.63	0.17	5.81	34.51	0.673	0.491
E4	0.51		0.72^**	50.59	21.23	0.16	5.07	32.37	0.560	1.009
荚果宽 PW (mm)	E1	0.61	0.82^**	19.20	10.22	0.13	1.84	14.53	0.192	-0.004
	E2	0.57	0.95^**	18.76	8.76	0.16	2.10	13.40	0.370	-0.292
	E3	0.60	0.63^**	22.31	9.46	0.14	1.96	14.02	0.489	0.787
	E4	0.53	0.87^**	17.64	9.41	0.13	1.76	13.33	-0.005	-0.336
荚果厚 PT (mm)	E1	0.49	0.78^**	18.98	9.69	0.13	1.91	14.25	0.166	-0.189
	E2	0.42	0.69^**	20.23	8.73	0.16	2.09	12.91	0.871	0.392
	E3	0.55	0.81^**	19.59	9.04	0.13	1.82	13.82	-0.016	0.218
	E4	0.34	0.82^**	16.91	8.91	0.12	1.62	13.52	-0.226	-0.353
百果重 HPW (mm)	E1	5.68	4.97^**	314.00	61.40	0.29	44.96	155.85	0.583	0.024
	E2	5.41	3.42^**	227.00	63.00	0.29	37.60	130.54	0.257	-0.419
	E3	4.32	3.01^**	296.00	56.00	0.28	47.12	167.34	0.414	0.166
	E4	4.26	5.51^**	212.00	52.00	0.29	35.65	123.53	0.359	-0.225

环境Environment	性状Trait	荚果长PL	荚果宽PW	荚果厚PT
E1	荚果宽PW	0.349^***
	荚果厚PT	0.302^***	0.914^***
	百果重HPW	0.636^***	0.774^***	0.768^***
E2	荚果宽PW	0.373^***
	荚果厚PT	0.363^***	0.854^***
	百果重HPW	0.532^***	0.788^***	0.670^***
E3	荚果宽PW	0.171^***
	荚果厚PT	0.240^***	0.856^***
	百果重HP图W	0.574^***	0.610^***	0.697^***
E4	荚果宽PW	0.312^***
	荚果厚PT	0.482^***	0.883^***
	百果重HPW	0.524^***	0.731^***	0.705^***

性状 Trait		上位性QTL E-QTL	染色体 Chr.	位置1 Pos. 1	标记区间1 Marker interval 1	上位性QTL E-QTL	染色体 Chr.	位置2 Pos. 2	标记区间2 Marker interval 2	LOD	贡献率 PVE (%)
荚果长 PL (mm)	E3	E-qPLA03	A03	0	A03_71003-621044	E-qPLB04	B04	5	B04_1300271-2726314	5.40	21.84
荚果长 PL (mm)	E4	E-qPLA05	A05	210	A05_16823212-17149189	E-qPLB10	B10	205	B10_148392050-148148634	6.67	15.98
荚果宽 PW (mm)	E1	E-qPWB04	B04	30	B04_4064597-8111568	E-qPWB05	B05	70	B05_28723528-31732034	5.39	16.03
	E1	E-qPWA08	A08	65	A08_29556435-29781487	E-qPWB08	B08	65	B08_126197151-126599602	5.36	16.70
	E2	E-qPWA04.1	A04	145	A04_108410606-108792245	E-qPWA07	A07	470	A07_164614645-164794252	5.12	13.85
	E3	E-qPWA04.2	A04	145	A04_108410606-108792245	E-qPWA08	A08	40	A08_9856553-10239337	6.24	16.11
荚果厚 PT (mm)	E1	E-qPTA04	A04	145	A04_108410606-108792245	E-qPTA07	A07	470	A07_164614645-164794252	5.99	19.36
	E2	E-qPTA09	A09	115	A09_75588894-106054640	E-qPTA10	A10	125	A10_3847294-4076607	5.50	4.40
	E2	E-qPTA08	A08	65	A08_29556435-29781487	E-qPTB01.1	B01	75	B01_31459252-41455928	6.33	5.01
	E2	E-qPTA10	A10	125	A10_3847294-4076607	E-qPTB02.2	B01	75	B01_31459252-41455928	5.46	4.49
	E2	E-qPTB01.1	B01	70	B01_31459252-41455928	E-qPTB04	B04	60	B04_77304078-87562376	5.07	4.33
	E2	E-qPTB01.2	B01	75	B01_31459252-41455928	E-qPTB09	B09	80	B09_155190824-158481352	5.26	4.21
百果重 HPW (g)	E3	E-qHPWA03	A03	0	A03_71003-621044	E-qHPWA05	A05	240	A05_28575794-29060303	6.47	18.17
百果重 HPW (g)	E3	E-qHPWB02	B02	165	B02_34558390-102335914	E-qHPWAB08	B08	10	B08_2544346-2638685	5.24	13.54

基因ID Gene ID	染色体 Chr.	标记区间 Marker interval (bp)	基因家族 Gene family	基因功能注释 Gene functional description
Ahy_A08g039614	A08	30126461-30179893	legfed_v1_0.L_8Q8YMG	自噬相关蛋白8 Autophagy protein 8
Ahy_A08g039622	A08	30271630-30271880	legfed_v1_0.L_56M8PD	热休克蛋白90 Heat shock protein 90
Ahy_A08g039624	A08	30283347-30291196	legfed_v1_0.L_2H8YNS	顺乌头酸酶Aconitase
Ahy_B02g057589	B02	4893488-4896861	legfed_v1_0.L_Q5KQS5	吡哆胺-5'-磷酸氧化酶 Pyridoxamine 5'-phosphate oxidase
Ahy_B02g057608	B02	5171380-5171736	legfed_v1_0.L_9WDQD0	EF手型结构域钙结合蛋白 EF-hand calcium-binding proteins
Ahy_B02g057640	B02	5652666-5658241	legfed_v1_0.L_29W3YK	丝氨酸/苏氨酸蛋白激酶 Serine/Threonine kinase proteins
Ahy_B02g057642	B02	5756798-5758215	legfed_v1_0.L_KCL7Q5	b HLH转录因子 Basic helix-loop-helix transcription factor
Ahy_B02g057660	B02	5907035-5918712	legfed_v1_0.L_0C0SD2	BRO 1结构域蛋白 BRO domain-containing protein 1
Ahy_B02g057673	B02	6069768-6073611	legfed_v1_0.L_1GQHGD	3-酮酯酰-CoA合酶 3-ketoacyl-CoA synthases
Ahy_B06g085840	B06	147106411-147106976	legfed_v1_0.L_0JZZ84	聚酮环化酶2 Polyketide cylcases 2
Ahy_B06g085859	B06	147357241-147378643	legfed_v1_0.L_5MH5QP	早花3转录因子Early flowering 3
Ahy_B06g085890	B06	147787935-148593101	legfed_v1_0.L_YFP2RZ	AP2类乙烯反应转录因子 AP2-like ethylene-responsive transcription factor

QTL mapping and candidate gene analysis of peanut pod yield-related traits

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