小麦主栽品种济麦22与良星99的基因组序列多态性比较分析

doi:10.3724/SP.J.1006.2020.01009

Abstract

Abstract:

Jimai 22 and Liangxing 99 are high-yield wheat varieties widely planted in the North Huang-Huai Rivers Valley Winter Wheat Zone and Northern Winter Wheat Zone in China, and are currently used as important parents in wheat breeding programs. Although the origins and pedigrees of Jimai 22 and Liangxing 99 are different, they are highly similar in many important agronomic traits, yield-associated traits, and so on. To identify the genomic differences between the two varieties, we performed whole-genome sequencing using the Illumina HiSeq2500 platform, with an average sequencing depth of 5.8×. We aligned the raw sequencing data against the Chinese Spring reference genome and identified the difference of copy-number variation (CNV) regions, single-nucleotide polymorphisms (SNPs) and InDels in sequence between the two varieties. Lengths of 466 Mb CNV intervals were shared by the two varieties. The lengths of cultivar-specific CNV intervals in Jimai 22 and Liangxing 99 were 91 Mb and 45 Mb, respectively, and these intervals are mainly located on chromosomes 2B and 4B. Beyond the CNV intervals, 1,547,371 SNPs and 137,817 InDels were different between the two cultivars. Based on the distribution of SNP densities in the intervals, we identified the polymorphic hotspot regions on chromosomes 1D, 2B, and 4B, making up 14.2% of the whole genome. The sequences of five previous cloned dwarf genes and spike length related genes were investigated, and two genes located in the polymorphic hotspot regions were detected with the frame shift variations. This study provides an important guidance for evaluating the genetic differences between two wheat varieties in the genomic level, and also identified both genetic similarity regions and polymorphic hotspot regions between Jimai 22 and Liangxing 99, which provided a valuable genetic information for future genetic improvement utilizing Jimai 22 and Liangxing 99 as parents.

Key words: wheat, Jimai 22, Liangxing 99, whole-genome resequencing, SNP, CNV

YANG Zheng-Zhao, WANG Zi-Hao, HU Zhao-Rong, XIN Ming-Ming, YAO Ying-Yin, PENG Hui-Ru, YOU Ming-Shan, SU Zhen-Qi, GUO Wei-Long. Comparative analysis of the genomic sequences between commercial wheat varieties Jimai 22 and Liangxing 99[J].Acta Agronomica Sinica, 2020, 46(12): 1870-1883.

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引物编号 Primer ID	引物序列 Primer sequence (5'-3')	退火温度 Annealing temperature (℃)	用途 Purpose
TraesCS2D02G055700_F	CAGGTCGAGACAGAGAACAA	56	测序引物 Sequencing primers
TraesCS2D02G055700_R	ATCGAGCCCCTCAATTTCAT	58	CNV标记特异引物 Specific primers for CNV markers
TraesCS2D02G051500_F	TCAGCTCAGGGTTATCAAGC
TraesCS2D02G051500_R	TTGGGTGCATTTTTCAGTCC
2B_LX99_CNV1_F	AGCAGGTAATCCACACCAAA
2B_LX99_CNV1_R	TGGAGAACCCACTTATCCAA
2B_LX99_CNV2_F	AGCAGGTAATCCACACCAAA
2B_LX99_CNV2_R	AATCCACACCAAATCCCCAT
2B_COM_CNV_F	CACCCTAGATACAACCGAGG
2B_COM_CNV_R	ATGTCACCGATCTTCTGAGC
2D_COM_CNV_F	ATGATCACGATGGACCTAGC
2D_COM_CNV_R	TGCCACGAAGATTTAGAGGA

表型 Phenotype	济麦22 Jimai 22		良星99 Liangxing 99		差异显著性 Statistical significance of the difference
表型 Phenotype	均值±标准误差 Mean ± SE	样本量 Sample counts	均值±标准误差 Mean ± SE	样本量 Sample counts	P-value (t-test)
旗叶长Flag leaf length (cm)	16.78±0.36	30	16.94±0.40	30	0.76
旗叶宽Flag leaf width (cm)	1.88±0.024	30	1.85±0.039	30	0.53
每穗小穗数Spikelet number per spike	21.87±0.45	30	21.80±0.28	30	0.91
每穗可育小穗数Fertile spikelet per spike	21.23±0.50	30	21.17±0.14	30	1.00
每穗不育小穗数Infertile spikelet per spike	0.63±0.14	30	0.63±0.23	30	0.90
穗长Spike length (cm)	9.57±0.13	30	10.43±0.15	30	3.98E-5 ^**
株高Plant length (cm)	75.05±0.57	30	80.23±0.75	30	1.90E-6 ^**
穗粒数Grain number per spike	52.23±0.73	30	55.20±0.35	30	0.31
千粒重Thousand seed weight (g)	49.20±0.33	6	48.30±0.03	6	0.66
粒长Grain length (cm)	6.43±0.07	6	6.53±0.03	6	0.39
粒宽Grain width (cm)	3.25±0.06	6	3.30±0.02	6	0.58

基因组 Genome	济麦22中的纯合 SNP个数 Number of homozygous SNPs in Jimai 22	良星99中的纯合 SNP个数 Number of homozygous SNPs in Liangxing 99	两者基因型相同的纯合SNP个数 Number of homozygous SNPs with the same genotype	两者基因型不同的纯合 SNP个数 Number of homozygous SNPs with different genotypes
A	6,405,063	6,395,080	6,194,047	301,206
B	8,033,789	7,781,369	7,248,448	1,148,764
D	887,462	883,555	818,951	97,401
全基因组 Whole genome	15,326,314	15,060,004	14,261,446	1,547,371

基因组 Genome	济麦22中的纯合 InDel个数 Number of homozygous InDels in Jimai 22	良星99中的纯合 InDel个数 Number of homozygous InDels in Liangxing 99	两者基因型相同的纯合InDel个数 Number of homozygous InDels with the same genotype	两者基因型不同的纯合 InDel个数 Number of homozygous InDels with different genotypes
A	464,369	459,599	438,410	28,732
B	562,658	543,395	492,112	95,316
D	116,485	115,570	104,345	13,769
全基因组Whole genome	1,143,512	1,118,564	1,034,867	137,817

基因组 Genome	济麦22的特有CNV区间 Specific CNV region in Jimai 22		良星99的特有CNV区间 Specific CNV region in Liangxing 99		两品种的共有CNV区间 Common CNV regions in the two cultivars
基因组 Genome	长度 Length (Mb)	%	长度 Length (Mb)	%	长度 Length (Mb)	%
A	8	0.06	4	0.03	135	0.96
B	80	0.57	33	0.23	226	1.61
D	3	0.02	8	0.06	105	0.75
全基因组Whole genome	91	0.65	45	0.32	466	3.31

Comparative analysis of the genomic sequences between commercial wheat varieties Jimai 22 and Liangxing 99

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