旱地小麦穗粒数全基因组关联分析与候选基因发掘

doi:10.3864/j.issn.0578-1752.2026.17.002

Abstract

Abstract:

【Objective】Wheat (Triticum aestivum L.) ranks among the most vital cereal crops globally, making the enhancement of its yield crucial for ensuring food security. The grain number per spike (GNS) serves as a critical determinant of wheat yield. Understanding the genetic architecture of GNS and identifying key candidate genes will promote genetic improvement and enable marker-assisted selection for this trait.【Method】A panel of 123 wheat accessions was phenotyped for GNS across multiple drought-prone environments. Genome-wide association studies (GWAS) were conducted utilizing a mixed linear model (MLM) based on genotyping data derived from a 35K SNP array. For marker-trait associations (MTAs) significantly correlated with GNS, haplotype analysis was performed, Kompetitive Allele-Specific PCR (KASP) markers were developed, and multi-environment phenotypic validation was executed. Candidate genes were identified through public RNA-seq data to screen for genes with high expression levels in spike tissues. This was followed by validation using quantitative real-time reverse transcription PCR (qRT-PCR) and functional annotation based on homology and previously reported functional information.【Result】GNS exhibited coefficients of variation between 17.18% and 22.48% across different environments, indicating a significant environmental impact. The GWAS identified 47 significant MTAs, with the highest concentration of 9 MTAs located on chromosome 5A. Notably, the marker AX-94445381 on chromosome 5A was consistently detected in two environments, demonstrating a stable genetic association. Haplotype analysis categorized this marker into two distinct haplotypes (HapⅠ and HapⅡ). Validation of the KASP marker indicated that accessions carrying HapⅡ displayed significantly higher GNS across three environments compared to those with HapⅠ. An analysis of the favorable haplotype AX-94445381-HapⅡ, utilizing publicly available resequencing data, revealed that its frequency was lower in modern cultivars (30.1%) than in landraces (40.0%), suggesting that this haplotype has not been fully exploited in wheat breeding programs. Candidate gene screening within the 1 Mb region surrounding AX-94445381, in conjunction with RNA-seq data, identified genes that are highly expressed specifically in spike tissue. Validation through qRT-PCR and homology analysis with rice orthologs identified three candidate genes directly involved in spike development, which encode a UDP-glycosyltransferase, a MADS-box transcription factor, and a WD repeat-containing protein, respectively.【Conclusion】A major stable locus, AX-94445381, associated with GNS has been identified. The advantageous haplotype AX-94445381-HapⅡ was shown to markedly enhance GNS, underscoring its potential for further exploitation and application in wheat breeding.

Key words: wheat, grain number per spike, genome-wide association study, KASP marker, candidate genes

WANG HaoDong, WANG Peng, WU YuXuan, ZHANG Qin, WANG QiaoYun, GUO LiJian, YANG DeLong, CHEN Tao. Genome-Wide Association Study and Candidate Gene Identification for Grain Number per Spike in Dryland Wheat (Triticum aestivum L.)[J].Scientia Agricultura Sinica, 2026, 59(17): 3712-3729.

Figures/Tables 17

Fig. 1

Table 1

Table 2

Fig. 2

Table 3

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Table 5

MTA associated with GNS detected by GWAS"

标记Marker	等位变异Allelic variation	染色体Chr.	物理位置Position (bp)	环境Environment	P值P value	R² (%)
AX-94940774	G/T	1A	412035140	E3	3.71E-04	12.69
AX-94595074	A/G	1B	1434729	E2	4.28E-04	14.29
AX-94460586	C/T	2A	568411263	E2	2.52E-04	14.39
AX-94918833	G/T	2A	740873736	E3	3.10E-04	13.95
AX-94773990	C/T	2A	31089755	E3	7.14E-04	14.08
AX-94905029	A/G	2A	52586827	E4	7.04E-04	13.14
AX-95126447	A/G	2A	24060452	E4	7.20E-04	13.55
AX-94970086	C/G	2B	680522418	E1	1.30E-04	16.48
AX-94450454	A/G	2B	738686815	E2	8.58E-05	16.72
AX-94408488	C/T	2B	580887157	E2	3.16E-04	13.91
AX-94431990	A/C	2B	657793077	E2	5.19E-04	13.06
AX-95256964	A/G	2B	737490832	E2	6.45E-04	12.66
AX-94450445	A/G	3B	783870123	E3	3.30E-04	16.08
AX-94783697	A/C	4B	581072860	E2	4.15E-04	13.27
AX-95127411	A/T	4B	573290876	E4	8.46E-04	10.46
AX-94472979	A/G	5A	551483456	E1	4.72E-04	15.27
AX-94479272	C/G	5A	552515382	E1	7.24E-04	13.06
AX-95243984	A/G	5A	549800941	E1	7.90E-04	13.23
AX-94522762	C/T	5A	485598127	E2	4.07E-04	14.71
AX-94445381	A/C	5A	588738568	E3	3.38E-04	13.83
AX-94445381	A/C	5A	588738568	E4	3.99E-04	14.02
AX-94404219	A/C	5A	588854488	E3	6.30E-04	13.74
AX-95085015	A/C	5A	480284549	E4	2.44E-04	14.79
AX-95629907	A/G	5A	480176958	E4	4.33E-04	13.72
AX-94615284	A/T	5A	479848189	E4	6.85E-04	14.04
AX-94712641	C/G	5B	691797180	E2	3.81E-04	13.48
AX-94820753	C/T	5B	689950369	E2	3.97E-04	13.53
AX-94878420	G/T	5B	449201643	E2	5.32E-04	12.82
AX-94977236	A/C	5D	408304024	E2	3.97E-04	13.60
AX-94431816	G/T	5D	545932823	E2	4.07E-04	13.26
AX-95114243	C/G	5D	375310485	E2	4.19E-04	13.23
AX-94395064	A/G	6A	73994641	E2	4.38E-04	13.51
AX-94750824	A/G	6A	25692809	E2	8.20E-04	12.07
AX-94660514	A/G	6A	65066575	E3	7.25E-04	15.86
AX-94982674	G/T	6A	559432410	E3	7.78E-04	12.85
AX-94624630	G/T	6A	108070104	E4	9.10E-04	13.33
AX-94511580	A/T	6B	191529940	E2	2.67E-04	14.64
AX-94758158	C/T	6B	492492877	E2	7.01E-04	12.29
AX-94708023	C/T	6B	21138180	E3	2.16E-04	16.89
AX-94898852	C/T	6B	462157403	E3	8.90E-04	12.28
AX-95252437	G/T	6D	55925493	E1	9.43E-04	12.53
AX-95222417	C/T	6D	9972857	E2	2.14E-04	16.19
AX-94759612	C/T	6D	200873028	E2	3.73E-04	13.44
AX-94572243	A/G	6D	80064488	E3	6.84E-04	14.55
AX-94675786	C/T	7A	21446154	E2	5.21E-04	12.81
AX-94389135	A/C	7A	713743759	E2	9.81E-04	11.80
AX-94456211	A/G	7A	30816891	E3	5.81E-04	14.12
AX-94467530	G/T	7B	537458194	E1	9.01E-04	10.29

Table 5

Fig. 6

Fig. 7

Fig. 8

Fig. 9

Fig. 10

Fig. 11

Table 6

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引物Primer	序列Sequence (5′-3′)
AX-94445381-KASP-F1	GAAGGTGACCAAGTTCATGCTTTGGAAGGATTCGGCACGCA
AX-94445381-KASP-F2	GAAGGTCGGAGTCAACGGATTTTGGAAGGATTCGGCACGCC
AX-94445381-KASP-R	CAGCCAGCCCTTGCCTCCGTGC

基因ID Gene ID	正向引物 Forward primer (5′-3′)	反向引物 Reverse primer (5′-3′)
TraesCS5A02G391800	GATGCTGCCGTGCCGACTACC	GACCCTCAAGCTGTTCAAGCTCG
TraesCS5A02G392400	AGAACCTCACGCAGGCCGCCG	CCGCCAGCACCGGAGTCAAAC
TraesCS5A02G392600	CGTCGCCTCTCTCAGTAACCTCC	GAATAGCCATGCCCGGAGAGC
TraesCS5A02G393000	GAGGGAGAGATTCCGGAGAGTGTC	CGACACTGCCCTAGCTCCCTAG
TraesCS5A02G393500	GAAGGCGAAGGGGTCACTGGAC	GATTTGGGCACCACGCGCGTC
TraesCS5A02G393700	CCGGGCTTGCCAGTACAGTTATCC	CCGGTGCTAGAGGCTGAAGTGG
TraesCS5A02G394200	GTCCAACCGAAGGGCAGCAGCTG	CGGAGCTCCTGGTCGGCAAAC
TaGAPDH	AAATCTGGCATCACACTTTCTAC	GTCTCAAACATAATCTGGGTCATC

性状 Trait	环境 Environment	范围 Range	平均值±标准差 Mean±SD	变异系数 CV (%)	偏度 Skewness	峰度 Kurtosis
穗粒数 GNS	E1	18.00-58.00	39.59±7.85	19.83	-0.013	-0.039
	E2	20.33-53.00	34.32±5.89	17.18	0.404	0.940
	E3	13.67-59.33	33.94±7.63	22.48	0.409	-0.442
	E4	26.00-66.67	43.61±8.29	19.01	0.650	-0.123

染色体 Chr.	标记数目 No. of markers	物理长度 Physical length (Mb)	标记密度 Marker density (Mb)	最小等位基因频率MAF		多态性信息含量PIC
染色体 Chr.	标记数目 No. of markers	物理长度 Physical length (Mb)	标记密度 Marker density (Mb)	均值Average	范围Range	均值Average	范围Range
1A	812	592.86	0.73	0.75	0.50-0.95	0.27	0.09-0.38
1B	924	688.60	0.75	0.74	0.50-0.95	0.29	0.09-0.38
1D	616	495.13	0.80	0.76	0.50-0.95	0.27	0.09-0.38
2A	854	780.32	0.91	0.76	0.50-0.95	0.26	0.09-0.38
2B	980	799.42	0.82	0.75	0.50-0.95	0.27	0.09-0.38
2D	709	651.40	0.92	0.74	0.50-0.95	0.28	0.09-0.38
3A	621	749.26	1.21	0.74	0.50-0.95	0.28	0.09-0.38
3B	875	829.07	0.95	0.74	0.50-0.95	0.28	0.09-0.38
3D	391	613.59	1.57	0.74	0.50-0.95	0.28	0.09-0.38
4A	453	742.10	1.64	0.77	0.50-0.95	0.26	0.09-0.38
4B	444	672.67	1.52	0.78	0.50-0.95	0.25	0.09-0.38
4D	181	508.05	2.81	0.74	0.50-0.95	0.28	0.09-0.38
5A	685	708.54	1.03	0.73	0.50-0.95	0.29	0.09-0.38
5B	912	712.88	0.78	0.74	0.50-0.95	0.28	0.09-0.38
5D	478	565.85	1.18	0.73	0.50-0.95	0.28	0.09-0.38
6A	635	617.28	0.97	0.73	0.50-0.95	0.28	0.09-0.38
6B	717	720.60	1.01	0.74	0.50-0.95	0.28	0.09-0.37
6D	383	473.37	1.24	0.76	0.50-0.95	0.27	0.09-0.38
7A	694	736.45	1.06	0.77	0.50-0.95	0.26	0.09-0.38
7B	550	750.49	1.36	0.77	0.50-0.95	0.26	0.09-0.38
7D	388	634.71	1.64	0.77	0.50-0.95	0.26	0.09-0.38
A基因组Genome A	4754	4926.81	1.04	0.75	0.50-0.95	0.27	0.09-0.38
B基因组Genome B	5402	5173.73	0.96	0.75	0.50-0.95	0.27	0.09-0.38
D基因组Genome D	3146	3942.10	1.25	0.75	0.50-0.95	0.27	0.09-0.38
总计Total	13302	14042.64	1.06	0.75	0.50-0.95	0.27	0.09-0.38

候选基因 Candidate gene	基因区间 Gene interval (bp)	基因注释 Gene annotation	水稻基因号 Rice gene number	同源性 Homology (%)	E值 E value
TraesCS5A02G391800	588017833-588024080	MADS-box转录因子 MADS-box transcription factor	LOC_Os03g54170	97	1.24E-118
TraesCS5A02G391800	588017833-588024080	MADS-box转录因子 MADS-box transcription factor	LOC_Os06g06750	96	2.54E-71
TraesCS5A02G392400	588553923-588558813	WD重复序列蛋白 WD repeat-containing protein	LOC_Os03g51550	73	6.64E-29
TraesCS5A02G394200	589370600-589373630	UDP-糖基转移酶 UDP-glycosyltransferase	LOC_Os03g55040	93	8.82E-116
TraesCS5A02G392600	588740101-588746176	ABC转运蛋白B家族蛋白 ABC transporter B family protein	LOC_Os03g54790	100	0.0
TraesCS5A02G393000	588871831-588876487	受体蛋白激酶Receptor protein kinase	LOC_Os07g41140	96	0.0
TraesCS5A02G393500	589240694-589244001	有丝分裂纺锤体组织蛋白1B Mitotic-spindle organizing protein 1B	LOC_Os03g32150	91	2.96e-13
TraesCS5A02G393700	589287682-589295519	牙本质唾液磷蛋白 Dentin sialophosphoprotein-like protein	LOC_Os03g54970	61	2.03e-136

Genome-Wide Association Study and Candidate Gene Identification for Grain Number per Spike in Dryland Wheat (Triticum aestivum L.)

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