基于SSR标记的谷子主要农艺性状关联位点检测及等位变异分析

doi:10.3864/j.issn.0578-1752.2019.24.002

Abstract

Abstract:

【Objective】Through the investigation of 10 major traits in foxtail millet at Ledong, Hainan province, Luoyang, Henan province, Jilin and Gongzhuling, Jilin province, totally four different geographical environments, association analysis between SSR markers and the ten traits was performed to obtain loci expressed in single environment or multiple environments, excavate elite allelic variations, explore the probable mechanism forming ecological adaptation and provide foundation for launching molecular-assistant selection breeding in foxtail millet.【Method】Based on the survey of ten traits (plant height, panicle length, number of leaves, panicle diameter, heading stage, spikelet number, grain number per branch, spike weight, grain weight per panicle and 1000-grain weight) from 102 foxtail millet varieties at Jilin and Gongzhuling, Jilin province, Luoyang, Henan province and Ledong, Hainan province for two consecutive years, correlation analysis of ten traits at each geographical environment was first performed by SPSS 19.0 software, then the 102 foxtail millet varieties were genotyped by 70 polymorphic SSR markers, and further genetic diversity and population genetic structure of these varieties were analyzed. Finally, linkage disequilibrium analysis among markers and association analysis between molecular markers and phenotypic traits were carried out by GLM and MLM models of TASSEL 5.0 software. 【Result】There existed significant or very significant positive correlations among most of the nine agronomic traits except 1000-grain weight across four geographical environments. Only significant or very significant positive correlations were found between 1000-grain weight and grain weight per panicle, plant height, panicle length, spike weight at Jilin, Gongzhuling and Luoyang, no significant correlations were found between 1000-grain weight and other nine traits at Ledong environment. Totally 397 alleles were detected in 70 pairs of SSR primers, giving average observed allele number, effective allele number, expected heterozygosity, Shannon index of 6, 2.24, 0.4637 and 0.7738 per marker respectively. Both genetic diversity analysis and population structure analysis divided 102 foxtail millet materials into 4 groups, and the varieties from Henan province scattered in each of the four groups, showing more abundant genetic diversity. Linkage disequilibrium analysis showed that no obvious LD structures were found among 70 SSR markers. Totally 10 associated markers were detected by GLM and MLM models, combined with allele effect analysis results, it could be determined that b115, MPGC13, b227, b194 and p56 were associated with spike weight, panicle length, number of leaves and heading stage at Jilin, Gongzhuling, sigms9034 and b125 were associated with panicle length and spikelet number at Luoyang, P18 and p59 were associated with spike weight at Ledong, p6 was associated with number of leaves and spikelet number at Jilin, Gongzhuling and Luoyang respectively. The average contribution rates of single marker to phenotypic variation ranged from 7.76% to 34.05%. Three alleles, sigms9034-168, P18-166 and p56-244, could increase panicle length and spike weight, shorten heading stage significantly, which would be used to improve panicle traits and shorten growth period by marker-assisted selection breeding.【Conclusion】Five marker loci (b115, MPGC13, b227, b194 and p56) were steadily detected at Jilin and Gongzhuling, two marker loci (sigms9034, b125), two marker loci (P18, p59) were steadily detected at Luoyang and Ledong respectively for two consecutive years. One marker locus (p6) was steadily detected at Jilin, Gongzhuling and Luoyang, three geographical environments for two consecutive years. Three elite alleles (sigms9034-168bp, P18-166bp, p56-244bp) that could be used to carry out marker-assisted selection for panicle traits and growth period were obtained.

Key words: foxtail millet, SSR, geographical environment, agronomic traits, correlation analysis

JianFeng LI,Bo ZHANG,JianZhang QUAN,YongFang WANG,XiaoMei ZHANG,Yuan ZHAO,XiLei YUAN,XiaoPing JIA,ZhiPing DONG. Associated Loci Detection and Elite Allelic Variations Analysis of Main Agronomic Traits in Foxtail Millet (Setaria italica L.) Based on SSR Markers[J].Scientia Agricultura Sinica, 2019, 52(24): 4453-4469.

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URL: https://www.chinaagrisci.com/EN/10.3864/j.issn.0578-1752.2019.24.002

https://www.chinaagrisci.com/EN/Y2019/V52/I24/4453

Figures/Tables 9

品种编号 Variety number	品种名 Variety name	来源地 Origin area	品种编号 Variety number	品种名 Variety name	来源地 Origin area
HN1	郑05-1 Zheng05-1	中国河南 Henan, China	HB21	104 104	未知 Unknown
HN2	郑05-2 Zheng05-2	中国河南 Henan, China	HB22	200152 200152	未知 Unknown
HN3	安04-4705 An04-4705	中国河南 Henan, China	HB23	8322-14 8322-14	未知 Unknown
HN4	安04-4852 An04-4852	中国河南 Henan, China	HB24	冀谷32 Jigu32	中国河北 Hebei, China
HN5	安04-5014 An04-5014	中国河南 Henan, China	HB25	冀谷30 Jigu30	中国河北 Hebei, China
HN6	豫谷1 Yugu1	中国河南 Henan, China	HB26	冀谷28 Jigu28	中国河北 Hebei, China
HN7	安09-8525 An09-8525	中国河南 Henan, China	HB27	冀谷27 Jigu27	中国河北 Hebei, China
HN8	安08-4125 An08-4125	中国河南 Henan, China	HB28	95307 95307	中国河北 Hebei, China
HN9	郑07-2 Zheng07-2	中国河南 Henan, China	HB29	谷丰2 Gufeng2	中国河北 Hebei, China
HN10	郑谷2 Zhenggu2	中国河南 Henan, China	HB30	K325 K325	未知 Unknown
HN11	豫谷6 Yugu6	中国河南 Henan, China	HB31	白米1号 Baimi 1 hao	中国河北 Hebei, China
HN12	安10-4240 An10-4240	中国河南 Henan, China	HB32	冀谷1 Jigu1	中国河北 Hebei, China
HN13	郑07-1 Zheng07-1	中国河南 Henan, China	HB33	冀特5 Jite5	中国河北 Hebei, China
HN14	安10-4172 An10-4172	中国河南 Henan, China	HB34	坝谷139 Bagu139	中国河北 Hebei, China
HN15	豫谷17 Yugu17	中国河南 Henan, China	HB35	坝91-0079 Ba91-0079	中国河北 Hebei, China
HN16	豫谷11 Yugu11	中国河南 Henan, China	HB36	毛谷2 Maogu2	中国河北 Hebei, China
HN17	豫谷8 Yugu8	中国河南 Henan, China	HB37	大白谷 Dabaigu	中国河北 Hebei, China
HN18	郑06-6 Zheng06-6	中国河南 Henan, China	HB38	大九根齐 Dajiugenqi	中国河北 Hebei, China
HN19	豫谷3 Yugu3	中国河南 Henan, China	HB39	坝谷6 Bagu6	中国河北 Hebei, China
HN20	安4117 An4117	中国河南 Henan, China	HB40	四留钱 Siliuqian	中国河北 Hebei, China
HN21	安-4585 An-4585	中国河南 Henan, China	HB41	坝谷210 Bagu210	中国河北 Hebei, China
HN22	安5424 An5424	中国河南 Henan, China	SD1	鲁谷10 Lugu10	中国山东 Shandong, China
HN23	豫谷15 Yugu15	中国河南 Henan, China	SD2	早白糯 Zaobainuo	中国山东 Shandong, China
HN24	豫谷13 Yugu13	中国河南 Henan, China	SD3	济大粒2 Jidali2	中国山东 Shandong, China
HN25	豫谷16 Yugu16	中国河南 Henan, China	SD4	济叶冲4 Jiyechong4	中国山东 Shandong, China
HN26	豫谷18 Yugu18	中国河南 Henan, China	SD5	济叶冲20 Jiyechong20	中国山东 Shandong, China
HN27	郑州12 Zhengzhou12	中国河南 Henan, China	SD6	济长穗8 Jichangsui8	中国山东 Shandong, China
HN28	郑315 Zheng315	中国河南 Henan, China	SD7	济丰30 Jifeng30	中国山东 Shandong, China
HN29	郑8041 Zheng8041	中国河南 Henan, China	SD8	金线子 Jinxianzi	中国山东 Shandong, China
HN30	豫谷5 Yugu5	中国河南 Henan, China	SD9	鲁谷3 Lugu3	中国山东 Shandong, China
HN31	新农673 Xinnong673	中国河南 Henan, China	SD10	鲁谷7 Lugu7	中国山东 Shandong, China
HB1	谷丰1 Gufeng1	中国河北 Hebei, China	SD11	书香1号 Shuxiang1hao	中国山东 Shandong, China
HB2	71杂30-2 71za30-2	未知 Unknown	SC1	11郄961 11 xi 961	未知 Unknown
HB3	张庙谷选变Zhangmiaoguxuanbian	未知 Unknown	SC2	11郄1071 11 xi 1071	未知 Unknown
HB4	冀谷15 Jigu15	中国河北 Hebei, China	BJ1	06-766 06-766	中国北京 Beijing, China
HB5	冀谷17 Jigu17	中国河北 Hebei, China	BJ2	小早谷 Xiaozaogu	中国北京 Beijing, China
HB6	衡谷9 Jigu9	中国河北 Hebei, China	NMG1	小香米 Xiaoxiangmi	中国河北 Hebei, China
HB7	金谷1 Jingu1	中国河北 Hebei, China	NMG2	籼紫灰谷Shanzihuigu	中国内蒙古 Neimenggu, China
HB8	沧372 Cang372	中国河北 Hebei, China	NMG3	二白谷 Erbaigu	中国内蒙古 Neimenggu, China
HB9	沧369 Cang369	中国河北 Hebei, China	NMG4	黄玉3 Huangyu3	中国内蒙古 Neimenggu, China
HB10	冀谷29 Jigu29	中国河北 Hebei, China	SX1	呼和浩特大毛谷Huhehaotedamaogu	中国陕西 Shanxi, China
HB11	冀谷26 Jigu26	中国河北 Hebei, China	SX2	延谷4 Yangu4	中国陕西 Shanxi, China
HB12	冀谷24 Jigu24	中国河北 Hebei, China	SX3	红杆谷 Honggangu	中国陕西 Shanxi, China
HB13	冀谷22 Jigu22	中国河北 Hebei, China	MFGY1	ISE430 ISE430	美国 America
HB14	冀谷19 Jigu19	中国河北 Hebei, China	MFGY2	法谷28-81 Fagu28-81	法国 French
HB15	冀谷18 Jigu18	中国河北 Hebei, China	MFGY3	SET3/80 SET3/80	德国 Germany
HB16	冀谷31 Jigu31	中国河北 Hebei, China	MFGY4	ISE775 ISE775	印度 India
HB17	复12 Fu12	中国河北 Hebei, China	HCCR1	龙谷26 Longgu26	中国黑龙江 Heilongjiang, China
HB18	冀创1 Jichuang1	中国河北 Hebei, China	HCCR2	朝鲜谷子 Chaoxianguzi	朝鲜 Korea
HB19	2015 2015	中国河北 Hebei, China	HCCR3	谷绿早1 Gulvzao1	朝鲜 Korea
HB20	2013 2013	中国河北 Hebei, China	HCCR4	大王国 Dawangguo	日本 Japan

SSR标记 SSR markers	引物序列 Primer sequence (5’-3’)	SSR标记 SSR markers	引物序列 Primer sequence (5’-3’)
b115	F:GGTAGCGACGGATCTACAGC R:GCTAGCAAATGCTGTCATGG	b202	F:AGAGCCCACGTCAAACC R:AAACTGGACTAGAAGAAGCATAG
b116	F:GCAAGCGTGATGTCAGATTAT R:ATAGGATGGTGGAAGCCCA	b101	F:ATCTAGGTGCCGATGCGT R:TGTGGGAAGAAGCTAGGGAA
b122	F:ACTTCTTCCTTCCTTGCGG R:TGTGGGATTAAGGTGCATCG	b106	F:TGCTTTGCTCTCTTCTCTCA R:ACGGACGATGAGGAATTGT
b125	F:GCCATGAAACAGGTACAAAAGG R:GCATCCCCTTAATTTGTCAATG	p59	F:TAATTTTGTGGCGTGGGATG R:GCACTGGTTTTGTTGAATGG
p6	F:AAGGATGGAATTTGCCACTG R:TTTCGACGATTTGCTTCAAC	p98	F:ATTCATCAGTAGCACAGC R:TGGAACTAAGAACAGGAAAC
p5	F:CTTCCCTCCCTCCCTGAC R:CTGAGCTGAGCTGCCTTTG	p56	F:GATGTGTACGGGTTGCATTG R:TGGGTTTCAGGGCTCTCTC
p3	F:GCAGAAAGCATGCCGTAGTC R:GCTTGGAGTCCACATGGATAG	p61	F:CATCCGCGTCATCTGAATC R:ACCTGCTGCTATCCATCACC
p8	F:CGATCGAATGATCGATGAAC R:CCCTTTGTCCGATCACGTC	p68	F:CATGCGTTGATCGTTTGTG R:ACCACGCATTTACATGATCG
p10	F:CAATCACATCCGAGCATTTC R:CACCCACCGTGTTGATCTG	p74	F:CAACCTAGTTTGCCTCAGTTATTC R:AGTCACGTACATGGGTGCAG
p12x	F:ACGAGTCACAAATCACAGCAC R:ATGCCTGAGCGGAACGGAA	p80	F:GCCGTTGGATTTGATTATGG R:TGTGGTTAGTTTATGTGGCTTG
p16	F:TTTCTCCCTCTCTCGATTCC R:AAATTGGCGTGCTAACAACC	p87	F:ACCTTTGACAAACGAGACACG R:GTTCGACTTGCATTGACTGG
b127	F:CCTCAAGTCAGTGAGATGCAA R:CAGAGCTGTTTAATCCTTGTTCA	p89	F:GCCTGTCTGAAAATTCTCAATG R:AGACGTGACATTAGCGCTTG
b129	F:CACACTCTTCTCCCCTTTTCC R:ACGGTAACGGAGGATGGCTA	p88	F:CAAGCCACCCAGTCTAGAGG R:TTCATCAGAACTGCGCAAAC
b142	F:TGGTAAAACTCCCATATTGAGC R:GCCCCATCCTTGATAACAGA	p92	F:TGGAATTGGAACCCTTTCG R:GCCATGCAAACAGTACCATC
b147	F:CTACTGCCTTCTGGCCTCC R:GGGCATTCTTGCTTCAGTCA	p85	F:GAATTAGGCCGATGCACAAC R:ATCCTAACTGCATGGCAAGG
b158	F:GATGAGGAAAAGGTAGGTTGGA R:CTGCAACGTGCAGAACTACG	p100	F:AGTTGACACCACACATAACAA R:AGAATACTCCTACCTGCCAC
b161	F:GGCATAAAAGTAAAAACCAACCA R:ACCTGGCTTCTGTCAGTGAA	p95X	F:GTCTCTGATAGTGCTTGAGCG R:ACAGGGATGAAGGGCGATG
b163	F:CTCGGAAGCTCAGATTCTCC R:CACTTCCTGCAGCTCTCACA	p29	F:GATGAGCACACGTTGATTGG R:GGACTTCACCACCGAGATG
b165	F:GCTTTGGTTTGGTTTGGTTGG R:CCATTAGTCTCTGCCCTTGTT	p44	F:TTCCCGGAACAGACAAGAAC R:GCGTTGGAAGCCATGGAG
b166	F:CGCCCATACTACCCAACAG R:ACCTCACCTTCCACTCCTC	p42	F:GCGACTTTCCCCTTCCAATC R:TTCCTTTTGTTGGCTTCTCC
b194	F:CTGGGTTCCGTCTACCGTA R:CACACCCGAAGAGGCAAAG	p91	F:AGCTGTGCTCCTCTGATCTTG R:TAACGTGGGGATGCACTAGC
b200	F:CATCGATCTCAACCTGTCCTT R:ATGAGCCGTCATGTCACAAA	sigms11655	F:TCGTTTAAGCTGGAATTGGG R:AGAGTACCGTCGGCGTCTAA
b107	F:AGAACGAGGTGGTGTGTGG R:GGGTCTCACGCTCTCATCA	P18	F:TTCTCTCGTTGGAATTTTTGTG R:GGAACAGATATCCTTTTCACTCTT
b123	F:GGTGTTCTCCTGTGTGC R:AGAGTTATTTCCAGCATTAGTG	p20	F:GTGCCCGCTTAGCTTTAATC R:ATGCACGTGGGACCCATAC
b159	F:GCCAGTCCGAGATGGTTAAG R:AGCTCTAGCAGTTGGGGACA	p17x	F:CGGACACCTGAAAGACGAA R:GTCACTTGTTGTTGTTGCG
b190	F:GAAATTTCACAAGTGTTGGTG R:TGATCGGAGCAGAGTGTTGA	sigms9034	F:TGCTGGTCGCAGTACTTGAT R:TCCTCTGCTCTGCTCTCCTC
b234	F:GCCGCAACGAACAACCG R:CCTGTCCCTATCCCTGTCG	sigms10291	F:TCGTCTCCGTCAGTAATCCC R:GCAGCAGAAGCAGATGAGG
b255	F:GAGGACAGCGGCCATT R:CCTCCCTCCATTTACTTTGG	sigms11641	F:CACCATGGCCACCATATGTA R:TGGTTGCTCAGCATAGCCTT
b242	F:CACTACCACTGTTCCAGATCG R:CAGGGACCTTGCTTGCATAC	sigms11693	F:CTAATTTTGCATGTGCCAGG R:CCACATACACCATGAGGTTCC
b185	F:GCACGTGTGACTTTCCACAT R:GTGAATGGCACACGAAACTG	sigms11672	F:TAGTAAACTTGGGCCCATCC R:ATAACTTCTCCCCCACCACC
b227	F:TGATCTGGCAGAACGAACA R:CAATTCCTGGACCAATATGC	sigms10287	F:GACCGATTCCTTCCAAACAA R:TGTCAGCTGGAGATGGTGTC
b233	F:GCCACGCACACCAACTT R:CTCCCGCAGAACACGCA	MPGD46	F:GATGGGTCGTCGTTAGAGTTT R:GGAAAGGGAAAGGAAGATAGC
b258	F:GGGCCAATAATGGTTGCATA R:TTGCACATCCAAATCTTTCC	MPGD10	F:CATCTGTTGCTGCTGATGCT R:AATTCTCAAAAGAGAGACCCACTG
b153	F:ACCCAACACATTCTCCTGAA R:TGCTATCAAAATAGTGCTAGAAT	sigms11	F:AGATCCTCGCAGACTTCGTC R:TGCAATCACCAGAGAGAAGC
b187	F:TTGGACAAATGACGCTATGC R:CTGCATCAAATCAGGACCAC	MPGC13	F:CTGAAGCATTCGATAAACTAGCTG R:GTAGTGAAAAATGAGCAAGGGTCT

Table 1

Correlation analysis of main agronomic characters of millet at different geographical environments"

环境 Environments	性状Trait	HS	GW	PH	NL	PL	PD	SN	GN	SW	1000-GW
吉林市 Jilin	HS	1
	GW	-0.157	1
	PH	0.035	0.340**	1
	NL	0.538**	0.195	0.105	1
	PL	0.04	0.464**	0.530**	0.109	1
	PD	0.173	0.415**	0.012	0.366**	0.208	1
	SN	0.421**	0.101	0.116	0.299*	0.285*	0.033	1
	GN	-0.08	0.667**	0.129	0.283*	0.119	0.547**	-0.209	1
	SW	-0.09	0.957**	0.361**	0.254*	0.547**	0.478**	0.122	0.694**	1
	1000-GW	-0.315**	0.388**	0.242*	-0.226	0.321**	0.051	-0.269*	-0.005	0.382**	1
公主岭市 Gongzhuling	HS	1
	GW	0.367**	1
	PH	0.420**	0.343**	1
	NL	0.756**	0.552**	0.485**	1
	PL	0.329*	0.332**	0.686**	0.282*	1
	PD	0.571**	0.480**	0.173	0.520**	0.260*	1
	SN	0.363**	0.206	0.380**	0.342**	0.302*	-0.115	1
	GN	0.323*	0.657**	0.064	0.401**	0.077	0.594**	-0.170	1
	SW	0.437**	0.938**	0.373**	0.596**	0.395**	0.618**	0.132	0.674**	1
	1000-GW	-0.018	0.307*	0.383**	0.068	0.427**	0.092	0.202	0.012	0.384**	1
洛阳市 Luoyang	HS	1
	GW	0.552**	1
	PH	0.571**	0.575**	1
	NL	0.662**	0.742**	0.670**	1
	PL	0.338**	0.205	0.716**	0.333**	1
	PD	0.567**	0.688**	0.558**	0.761**	0.388**	1
	SN	0.565**	0.554**	0.667**	0.648**	0.513**	0.541**	1
	GN	0.281*	0.745**	0.302**	0.493**	-0.079	0.544**	0.180	1
	SW	0.619**	0.951**	0.672**	0.794**	0.363**	0.766**	0.614**	0.687**	1
	1000-GW	0.211	0.347**	0.343**	0.300**	0.330**	0.296**	0.264*	0.046	0.371**	1
乐东县Ledong	HS	1
	GW	0.623**	1
	PH	0.163	0.228*	1
	NL	0.771**	0.781**	0.230*	1
	PL	0.607**	0.754**	0.189	0.609**	1
	PD	0.665**	0.858**	0.244**	0.845**	0.613**	1
	SN	0.429**	0.553**	0.284*	0.534**	0.558**	0.442**	1
	GN	0.353**	0.735**	0.159	0.557**	0.364**	0.697**	0.132	1
	SW	0.622**	0.808**	0.292*	0.708**	0.672**	0.775**	0.557**	0.503**	1
	1000-GW	-0.003	0.194	-0.083	0.064	0.120	0.129	0.079	-0.008	0.122	1

Table 1

Table 2

Polymorphism of seventy SSRs among 102 foxtail millet accessions"

SSR标记 SSR markers	等位基因数 Allele number	有效等位基因数 Number of effective alleles	Shannon指数 Shannon index	期望杂合度 Expected heterozygosity
b115	6	2.005	0.618	0.350
b116	4	1.712	0.521	0.325
b122	5	2.200	0.719	0.431
b125	5	2.447	0.926	0.575
p6	4	2.059	0.738	0.468
p5	6	2.022	0.632	0.363
p3	8	2.776	1.026	0.602
p8	6	1.983	0.611	0.346
p10	5	2.204	0.786	0.494
p12x	8	2.226	0.767	0.448
p16	5	1.849	0.631	0.390
b127	7	2.355	0.765	0.438
b129	4	2.283	0.849	0.516
b142	7	2.595	0.903	0.522
b147	4	1.773	0.622	0.400
b158	5	2.148	0.784	0.495
b161	5	1.926	0.666	0.405
b163	4	1.909	0.568	0.332
b165	4	1.827	0.590	0.395
b166	4	1.943	0.685	0.442
b194	6	1.909	0.657	0.380
b200	6	2.277	0.802	0.470
b107	7	1.961	0.721	0.446
b123	6	2.426	0.872	0.520
b159	6	2.600	0.900	0.509
b190	5	1.933	0.696	0.433
b234	4	1.742	0.503	0.308
b255	6	2.434	0.816	0.469
b242	4	2.100	0.766	0.477
b185	4	2.153	0.803	0.512
b227	4	2.025	0.637	0.392
b233	5	2.354	0.895	0.558
b258	6	2.118	0.775	0.478
b153	5	2.497	0.854	0.498
b187	5	2.498	0.940	0.578
b202	7	2.329	0.790	0.449
b101	6	2.218	0.779	0.448
b106	8	2.325	0.775	0.448
p59	5	2.258	0.812	0.496
p98	4	2.177	0.728	0.443
p56	5	2.123	0.806	0.508
p61	4	1.671	0.498	0.319
p68	5	2.098	0.734	0.466
p74	5	2.366	0.825	0.515
p80	8	2.797	1.025	0.598
p87	8	3.092	1.118	0.642
p89	8	2.538	0.892	0.497
p88	8	2.832	0.974	0.560
p92	7	2.425	0.843	0.498
p85	6	2.286	0.838	0.503
p100	6	2.448	0.879	0.530
p95X	9	2.827	0.935	0.502
p29	7	2.714	0.964	0.534
p44	8	2.932	1.036	0.605
p42	7	2.785	0.989	0.567
p91	8	2.362	0.802	0.474
sigms11655	6	1.788	0.490	0.295
P18	3	1.519	0.439	0.279
p20	7	2.519	0.937	0.570
p17x	6	2.335	0.818	0.495
sigms9034	5	1.593	0.493	0.311
sigms10291	4	2.174	0.728	0.451
sigms11641	3	1.726	0.538	0.368
sigms11693	6	2.463	0.946	0.572
sigms11672	4	1.686	0.516	0.321
sigms10287	7	2.723	0.913	0.498
MPGD46	6	2.297	0.804	0.466
MPGD10	5	2.649	0.974	0.588
sigms11	6	2.390	0.883	0.522
MPGC13	5	1.794	0.599	0.355

Table 2

Fig. 1

Fig. 2

Fig. 3

Table 3

Fig. 4

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性状 Traits	关联标记 Associated markers	染色体 Chromosome	显著性检验值（P） Significance test value (P)	表型贡献率（R²） Phenotypic variation (R²)	环境 Environments	年份 Years	模型 Model
GW SW PL	b115	2	9.99E-04 0.021 9.99E-04 0.013 0.0317 1.54E-04	0.4355 0.2456 0.4661 0.2521 0.0807 0.2421	吉林Jilin 公主岭Gongzhuling 吉林Jilin 公主岭Gongzhuling 吉林Jilin 公主岭Gongzhuling	2015 2016 2015 2016 2015 2016	GLM MLM
NL	MPGC13	7	9.99E-04 9.99E-04	0.24 0.3156	吉林Jilin 公主岭Gongzhuling	2015 2016	GLM
PL PH NL SN	p6	8	9.99E-04 0.025 0.0057 0.0118 0.0123 8.46E-04 0.033 0.0171 0.0127 0.015	0.1958 0.1712 0.0718 0.1109 0.0701 0.1591 0.0778 0.0774 0.0943 0.1031	吉林Jilin 公主岭Gongzhuling 吉林Jilin 公主岭Gongzhuling 吉林Jilin 公主岭Gongzhuling 吉林Jilin 公主岭Gongzhuling 洛阳Luoyang 洛阳Luoyang	2015 2016 2015 2016 2015 2016 2015 2016 2015 2016	GLM MLM
PL	sigms9034	6	9.99E-04 0.009	0.2361 0.1898	洛阳Luoyang 洛阳Luoyang	2015 2016	GLM
PL SN	b125	5	0.026 0.014 0.0094 0.0073	0.2717 0.2409 0.1405 0.1645	洛阳Luoyang 洛阳Luoyang 洛阳Luoyang 洛阳Luoyang	2015 2016 2015 2016	GLM MLM
HS	b227	1	9.99E-04 9.99E-04 0.0372 0.0308	0.2460 0.3075 0.0999 0.0811	吉林Jilin 公主岭Gongzhuling 吉林Jilin 公主岭Gongzhuling	2015 2016 2015 2016	GLM MLM
HS	b194	9	0.01 0.032	0.1537 0.0874	吉林Jilin 公主岭Gongzhuling	2015 2016	MLM
HS	p56	2	0.0215 0.0204	0.1202 0.0936	吉林Jilin 公主岭Gongzhuling	2015 2016	MLM
SW	P18	5	0.0117 0.0039	0.0861 0.1044	乐东Ledong 乐东Ledong	2015 2016	MLM
SW	p59	未知 Unknown	0.0452 0.016	0.0894 0.1171	乐东Ledong 乐东Ledong	2015 2016	MLM

Associated Loci Detection and Elite Allelic Variations Analysis of Main Agronomic Traits in Foxtail Millet (Setaria italica L.) Based on SSR Markers

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