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作物学报 ›› 2020, Vol. 46 ›› Issue (12): 1870-1883.doi: 10.3724/SP.J.1006.2020.01009

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

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

杨正钊(), 王梓豪, 胡兆荣, 辛明明, 姚颖垠, 彭惠茹, 尤明山, 宿振起*(), 郭伟龙*()   

  1. 中国农业大学农学院 / 农业生物技术国家重点实验室 / 杂种优势研究与利用教育部重点实验室, 北京 100193
  • 收稿日期:2020-01-15 接受日期:2020-06-02 出版日期:2020-08-10 发布日期:2020-11-25
  • 通讯作者: 宿振起,郭伟龙
  • 基金资助:
    国家重点研发计划项目(2018YFD0100803);国家自然科学基金项目(31701415);中央高校基本科研业务费专项资助

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

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*()   

  1. College of Agronomy and Biotechnology / State Key Laboratory for Agrobiotechnology / Key Laboratory of Crop Heterosis and Utilization, Ministry of Education, China Agricultural University, Beijing 100193, China
  • Received:2020-01-15 Accepted:2020-06-02 Online:2020-08-10 Published:2020-11-25
  • Contact: SU Zhen-Qi,GUO Wei-Long
  • Supported by:
    National Key Research and Development Program of China(2018YFD0100803);National Natural Science Foundation of China(31701415);Chinese Universities Scientific Fund.

摘要:

济麦22和良星99是我国黄淮冬麦区和北部冬麦区大面积推广的高产小麦品种, 也是目前小麦杂交育种的重要亲本。虽然济麦22和良星99的来源和系谱不同, 但在重要农艺、产量等性状上存在较高的相似性。为了从全基因组水平研究其遗传组成的异同, 本研究采用Illumina HiSeq2500测序平台对上述两个品种进行了全基因组测序(平均测序深度为5.8×), 并系统地比较了两个品种拷贝数变异(CNV)、单核苷酸多态性(SNP)和插入/缺失(InDel)的序列差异。与中国春参考基因组序列相比, 两个品种除了具有总长466 Mb的共有CNV变异区间外, 济麦22和良星99的特有CNV变异区间的总长分别为91 Mb和45 Mb, 这些特有CNV区间主要集中在2B和4B染色体上; 济麦22和良星99间存在1,547,371个SNP差异位点和137,817个InDel差异位点。以差异SNP分布规律为依据, 在全基因组水平鉴定出济麦22和良星99间存在14.2%的差异多态性热点区间, 这些区间集中分布在1D、2B和4B染色体上。通过对5个控制小麦株高和穗长基因的序列分析, 发现有2个位于多态性热点区间的基因在品种间存在移码突变。本研究为利用重测序数据在基因组水平上比较小麦品种间遗传差异提供了重要参考, 同时揭示了济麦22和良星99在全基因组的遗传相似区间和差异区间, 为今后小麦育种改良中更好利用济麦22与良星99提供了重要遗传信息。

关键词: 小麦, 济麦22, 良星99, 全基因组重测序, SNP, CNV

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

附图1

济麦22(A)与良星99(B)全基因组reads覆盖度的密度分布直方图 X轴为经归一化的每1 Mb内的平均reads覆盖度; Y轴为覆盖度的密度。"

附图2

济麦22与良星99间的单区间差异SNP的密度分布图 X轴, 每Mb区间内差异SNP位点数的对数(以10为底); Y轴, 位点数的密度。"

表1

本研究使用的引物编号和序列"

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

图1

济麦22与良星99的表型比较 A: 济麦22 (左)与良星99 (右)的株高及节间长度比较; B: 济麦22 (上)与良星99 (下)的粒型比较。"

表2

济麦22与良星99的主要农艺性状差异显著性分析"

表型
Phenotype
济麦22
Jimai 22
良星99
Liangxing 99
差异显著性
Statistical significance of the difference
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

表3

济麦22与良星99的纯合SNP位点统计"

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

表4

济麦22与良星99的纯合InDel位点统计"

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

表5

济麦22与良星99的全基因组CNV区间长度统计"

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
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

图2

济麦22与良星99的CNV区间(相对于中国春参照基因组)在各染色体上的分布 绿色: 济麦22的特有CNV区间; 粉色: 良星99的特有CNV区间; 紫色: 济麦22与良星99的共有CNV区间。"

图3

利用PCR对济麦22(JM22)、良星99(LX99)和中国春(CS)中检测的CNV区间进行验证 2D_COM_CNV和2B_COM_CV分别为2D和2B染色体上共有区间序列设计的引物; 2B_LX99_CNV1和2B_LX99_CNV2为在2B染色体上良星99特有的CNV区间中序列设计的引物。每对引物对应的3个泳道从左到右分别为: 良星99(LX99)、济麦22(JM22)和中国春(CS)。"

图4

济麦22(A)与良星99(B)特有CNV区间中基因的GO富集分析结果 绿色: 生物过程; 紫色: 细胞组分; 橙色: 分子功能。"

图5

济麦22与良星99全基因组内多态性热点区间分布 A: 两品种间差异SNP位点中分布在多态性热点区间与序列相似区间的比例; B: 多态性热点区间与序列相似区间的长度在全基因组上的比例; C: 多态性热点区间与序列相似区间在全基因组分布。深蓝色: 多态性热点区间; 浅蓝色: 序列相似区间; 白色: CNV区间。"

图6

济麦22与良星99间多态性热点区间的基因GO富集分析结果 绿色: 生物过程; 紫色: 细胞组分; 橙色: 分子功能。"

图7

济麦22与良星99间多态性热点区间与序列相似区间中各自的InDel长度分布(A)和SNP突变类型(B) 深蓝: 多态性热点区间; 浅蓝: 序列相似区间。"

表6

济麦22与良星99全基因组差异纯合SNP的突变类型的统计"

SNP突变类型
Types of SNP
mutations
多态性热点区间
Differential genetic region
相似区间
Similar genetic region
全基因组
Whole genome region
数量
Counts
每Mb密度
Density per Mb
数量
Counts
每Mb密度
Density per Mb
数量
Counts
每Mb密度
Density per Mb
T>A 33,545 17.52 1701 0.15 35,246 2.62
A>T 33,868 17.69 1713 0.15 35,581 2.64
G>C 49,065 25.62 2020 0.17 51,085 3.79
C>G 49,521 25.86 1956 0.17 51,477 3.82
A>C 47,712 24.91 2089 0.18 49,801 3.70
T>G 47,862 24.99 1888 0.16 49,750 3.69
G>T 65,670 34.29 3204 0.28 68,874 5.11
C>A 66,047 34.49 3226 0.28 69,273 5.14
A>G 200,697 104.80 6364 0.55 207,061 15.37
T>C 201,236 105.08 6540 0.57 207,776 15.42
G>A 289,933 151.40 11,276 0.98 301,209 22.36
C>T 290,292 151.59 11,151 0.96 301,443 22.38
转换Transition 982,158 512.88 35,331 3.06 1,017,489 75.53
颠换Transversion 393,290 205.37 17,797 1.54 411,087 30.51
全部Total 1,375,448 718.25 53,128 4.60 1,428,576 106.04

表7

济麦22与良星99的纯合InDel变异的长度分布"

InDel类型
Types of InDel
InDel长度
Length of InDel
差异区间
Differential genetic region
相似区间
Similar genetic region
全基因组
Whole genome region
数量
Count
每Mb密度
Density per Mb
数量
Count
每Mb密度
Density per Mb
数量
Count
每Mb密度
Density per Mb
在济麦22中插入, 在良星99中丢失
Insertion in Jimai 22, deletion in Liangxing 99
1 34,031 17.77 7723 0.67 41,754 3.10
2 7259 3.79 3017 0.26 10,276 0.76
3 2664 1.39 1242 0.11 3906 0.29
4 1685 0.88 843 0.07 2528 0.19
5 701 0.37 419 0.04 1120 0.08
6 883 0.46 370 0.03 1253 0.09
7 453 0.24 225 0.02 678 0.05
8 476 0.25 216 0.02 692 0.05
9 363 0.19 153 0.01 516 0.04
≥10 4131 2.16 1599 0.14 5730 0.43
全部Total 52,646 27.49 15,807 1.37 68,453 5.08
在良星99中插入, 在济麦22中丢失
Insertion in Liangxing 99, deletion in Jimai 22
1 34,083 17.80 7796 0.67 41,879 3.11
2 7315 3.82 3037 0.26 10,352 0.77
3 2690 1.40 1190 0.10 3880 0.29
4 1710 0.89 785 0.07 2495 0.19
5 746 0.39 420 0.04 1166 0.09
6 832 0.43 356 0.03 1188 0.09
7 412 0.22 227 0.02 639 0.05
8 509 0.27 208 0.02 717 0.05
9 402 0.21 183 0.02 585 0.04
≥10 3993 2.09 1637 0.14 5630 0.42
全部Total 52,696 27.52 15,835 1.37 68,531 5.09

表8

济麦22与良星99的纯合点突变对蛋白编码功能影响的统计"

变异所在区间
Region of variations
错义突变
Missense mutation
同义突变
Synonymous mutation
移码突变
Frame-shift mutation
提前终止突变
Stop-gained mutation
终止子丢失突变
Stop-lost mutation
数量
Count
% 数量
Count
% 数量
Count
% 数量
Count
% 数量
Count
%
差异区间Different region 2981 51.3 2431 41.9 304 5.2 68 1.2 16 0.3
相似区间Similar region 348 44.7 330 42.4 94 12.1 6 0.8 0 0
全部Total 3329 50.6 2761 42.0 398 6.1 74 1.1 16 0.2

表9

小麦株高相关基因列表及在序列相似区间和多态性热点区间的分布"

株高基因/QTL
Plant height gene/QTL
基因编号
Gene ID
染色体
Chromosome
区间
Region
基因功能注释
Function annotation
序列差异类型
Variation type
Rht-B1 TraesCS4B02G043100 4B 多态性热点区间
Polymorphic hotspot regions
编码DELLA蛋白
DELLA protein-coding gene

None
Rht-D1 TraesCS4D02G040400 4D 相似区间
Genetic similar region
编码DELLA蛋白
DELLA protein-coding gene

None
Ppd-D1 TraesCS2D02G079600 2D 相似区间
Genetic similar region
编码PRRs蛋白
PRRs protein-coding gene

None
QPht/Sl.cau-2D.1 TraesCS2D02G051500 2D 多态性热点区间
Polymorphic hotspot regions
编码WRKY转录因子
WRKY transcription factor protein-coding gene
InDel
QPht/Sl.cau-2D.1 TraesCS2D02G055700 2D 多态性热点区间
Polymorphic hotspot regions
编码GRAS转录因子
GRAS transcription factor protein-coding gene
InDel, SNP

图8

TraesCS2D02G051500(A)与TraesCS2D02G055700(B)在中国春、济麦22和良星99中功能改变位点附近的核苷酸序列"

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