中国农业科学 ›› 2020, Vol. 53 ›› Issue (9): 1717-1729.doi: 10.3864/j.issn.0578-1752.2020.09.003
• 专题:限制性两阶段多位点全基因组关联分析法的应用 • 上一篇 下一篇
郝晓帅1,傅蒙蒙1,刘再东1,贺建波1(),王燕平2,任海祥2,王德亮3,杨兴勇4,程延喜5,杜维广2,盖钧镒1()
收稿日期:
2019-09-09
接受日期:
2020-01-02
出版日期:
2020-05-01
发布日期:
2020-05-13
通讯作者:
贺建波,盖钧镒
作者简介:
郝晓帅,E-mail:15850563928@163.com。
基金资助:
XiaoShuai HAO1,MengMeng FU1,ZaiDong LIU1,JianBo HE1(),YanPing WANG2,HaiXiang REN2,DeLiang WANG3,XingYong YANG4,YanXi CHENG5,WeiGuang DU2,JunYi GAI1()
Received:
2019-09-09
Accepted:
2020-01-02
Online:
2020-05-01
Published:
2020-05-13
Contact:
JianBo HE,JunYi GAI
摘要:
【目的】对东北大豆种质群体百粒重性状进行全基因组关联分析,全面解析中国大豆主产区百粒重QTL-等位变异遗传构成,为东北地区大豆籽粒大小遗传改良提供理论基础。【方法】以东北地区育种和生产上常用的290份大豆材料作为试验群体,于2013和2014年在东北第二生态亚区的克山、牡丹江、佳木斯和长春4个地点进行百粒重表型鉴定试验。利用RAD-seq方法对试验群体进行基因组测序分析,对原始SNP数据进行过滤及填补缺失数据后,最终获得了82 966个高质量的SNP标记。根据限制性两阶段多位点全基因组关联分析(restricted two-stage multi-locus genome-wide association analysis,RTM-GWAS)方法,首先构建获得15 546个具有复等位变异的SNPLDB标记,然后使用两阶段多位点模型对百粒重性状进行全基因组关联分析。对检测到的百粒重关联SNPLDB标记位点附近(50 kb范围内)的基因进行分析,根据基因内SNP与SNPLDB标记位点之间关联性的卡方测验,筛选可能与百粒重性状相关的候选基因并进行功能注释。最后基于检测的百粒重QTL-等位变异体系分析了不同熟期组材料间的遗传分化。【结果】试验群体百粒重变异范围为18.3—20.7 g,性状遗传率为92.3%。RTM-GWAS方法共检测到76个与大豆百粒重性状关联的SNPLDB标记位点,其中15个位点主效不显著,另外61个主效显著位点解释了65.40%的表型变异;68个与环境互作效应显著的位点解释了17.46%的表型变异,另外8个位点与环境互作效应不显著。在检测到的76个位点中有34个位点与已报道的30个百粒重QTL重叠,另外42个位点为本研究新检测百粒重位点。基于检测的SNPLDB标记位点,共筛选到137个百粒重相关候选基因,功能注释显示这些候选基因不仅参与大豆百粒重的调节,还参与了初级新陈代谢、蛋白质修饰、物质运输、胁迫响应和信号转导等。对各熟期组间QTL-等位变异的遗传分化分析显示,尽管熟期组间百粒重差异不明显,但其QTL-等位变异遗传结构却发生了新生和汰除的变化。【结论】RTM-GWAS方法能相对全面地解析东北大豆种质群体百粒重QTL-等位变异遗传构成。东北大豆种质群体百粒重由大量QTL调控,且QTL与环境互作效应大,QTL存在丰富的复等位变异。由RTM-GWAS方法建立的QTL-等位变异矩阵为群体遗传及演化研究提供了新工具。
郝晓帅,傅蒙蒙,刘再东,贺建波,王燕平,任海祥,王德亮,杨兴勇,程延喜,杜维广,盖钧镒. 东北大豆种质群体百粒重QTL-等位变异的全基因组解析[J]. 中国农业科学, 2020, 53(9): 1717-1729.
XiaoShuai HAO,MengMeng FU,ZaiDong LIU,JianBo HE,YanPing WANG,HaiXiang REN,DeLiang WANG,XingYong YANG,YanXi CHENG,WeiGuang DU,JunYi GAI. Genome-Wide QTL-Allele Dissection of 100-Seed Weight in the Northeast China Soybean Germplasm Population[J]. Scientia Agricultura Sinica, 2020, 53(9): 1717-1729.
表1
东北大豆种质群体百粒重次数分布及描述统计"
类型 Type | 百粒重100-seed weight (g) | N | 平均数 Mean | 变幅 Range | 遗传率 h2 | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
7 | 9 | 11 | 12 | 14 | 16 | 17 | 19 | 21 | 23 | 24 | 26 | 28 | 29 | 31 | |||||
环境Environment | |||||||||||||||||||
长春CC | 1 | 1 | 0 | 0 | 9 | 45 | 75 | 85 | 52 | 14 | 4 | 4 | 290 | 20.3 | 9.7-28.2 | 0.642 | |||
佳木斯JMS | 1 | 2 | 10 | 3 | 1 | 1 | 17 | 57 | 93 | 68 | 28 | 4 | 4 | 0 | 1 | 290 | 20.7 | 8.1-32.0 | 0.780 |
克山KS | 3 | 2 | 0 | 1 | 5 | 45 | 91 | 83 | 49 | 9 | 1 | 0 | 1 | 290 | 18.3 | 6.4-28.2 | 0.777 | ||
牡丹江MDJ | 2 | 0 | 0 | 0 | 10 | 48 | 98 | 85 | 39 | 4 | 3 | 0 | 1 | 290 | 19.9 | 6.7-28.9 | 0.726 | ||
Mean | 1 | 1 | 0 | 0 | 7 | 53 | 89 | 90 | 39 | 5 | 4 | 0 | 1 | 290 | 19.8 | 8.2-29.5 | 0.923 | ||
熟期组Maturity | |||||||||||||||||||
MG0 | 1 | 2 | 25 | 55 | 51 | 16 | 4 | 1 | 155 | 19.9 | 13.6-25.6 | ||||||||
MG00 | 1 | 0 | 0 | 0 | 6 | 11 | 15 | 10 | 2 | 45 | 20.3 | 9.9-24.8 | |||||||
MG000 | 3 | 3 | 5 | 3 | 1 | 15 | 20.4 | 18.8-21.8 | |||||||||||
MGI+II | 2 | 9 | 33 | 25 | 6 | 75 | 19.7 | 15.6-22.7 | |||||||||||
MG0+00+000 | 1 | 0 | 1 | 2 | 34 | 69 | 71 | 29 | 7 | 1 | 215 | 20.0 | 9.9-25.6 |
表2
东北大豆种质群体百粒重多年多点联合方差分析"
模型Model | 变异来源Source | 自由度DF | 均方MS | F | p |
---|---|---|---|---|---|
基因型×年份×地点 Genotype×Year×Location | 年份Year | 1 | 835.46 | 81.59 | <0.001 |
地点Location | 3 | 3156.29 | 493.80 | <0.001 | |
区组(年份,地点) Block(Year, Location) | 24 | 2.59 | 1.86 | 0.0068 | |
基因型Genotype | 289 | 146.47 | 13.74 | <0.001 | |
基因型×年份Genotype×Year | 289 | 9.10 | 2.65 | <0.001 | |
基因型×地点Genotype×Location | 867 | 5.22 | 1.41 | <0.001 | |
基因型×年份×地点Genotype×Year×Location | 849 | 3.70 | 2.65 | <0.001 | |
误差Error | 6791 | 1.40 | |||
基因型×环境 Genotype×Environment | 环境Environment | 7 | 1978.57 | 308.84 | <0.001 |
区组(环境) Block(Environment) | 24 | 2.59 | 1.86 | 0.0068 | |
基因型Genotype | 289 | 147.00 | 28.15 | <0.001 | |
基因型×环境Genotype×Environment | 2005 | 5.24 | 3.75 | <0.001 | |
误差Error | 6791 | 1.40 |
表3
大豆百粒重显著相关SNPLDB位点"
QTL | AN | 主效QTL | QTL×Env. a | QTL | AN | 主效QTL | QTL×Env. a | |||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
-lgP | R2 (%) | -lgP | R2 (%) | -lgP | R2 (%) | -lgP | R2 (%) | |||||
q-SW-1-1 | 2 | - | - | 6.07 | 0.10 | q-SW-12-1 | 2 | 7.95 | 0.08 | 6.99 | 0.11 | |
q-SW-1-2 | 2 | - | - | 3.47 | 0.06 | q-SW-12-2 | 8 | 4.34 | 0.07 | 4.63 | 0.24 | |
q-SW-1-3 | 2 | - | - | 2.55 | 0.05 | q-SW-12-3 | 4 | 5.30 | 0.06 | 20.46 | 0.35 | |
q-SW-2-1 | 5 | 2.87 | 0.04 | 7.60 | 0.21 | q-SW-12-4 | 2 | 2.27 | 0.02 | 3.83 | 0.07 | |
q-SW-2-2 | 3 | - | - | 2.85 | 0.06 | q-SW-12-5 | 2 | - | - | 3.50 | 0.06 | |
q-SW-2-3 | 5 | 203.54 | 2.40 | 11.07 | 0.26 | q-SW-13-1 | 6 | 150.15 | 1.76 | 20.04 | 0.42 | |
q-SW-2-4 | 2 | - | - | 2.29 | 0.05 | q-SW-13-2 | 7 | 76.04 | 0.90 | 46.13 | 0.80 | |
q-SW-2-5 | 2 | 13.60 | 0.14 | - | - | q-SW-13-3 | 5 | 28.30 | 0.33 | 14.53 | 0.31 | |
q-SW-2-6 | 2 | 3.00 | 0.03 | - | - | q-SW-13-4 | 4 | 102.12 | 1.16 | 10.74 | 0.23 | |
q-SW-3-1 | 3 | 5.73 | 0.06 | - | - | q-SW-14-1 | 7 | - | - | 7.12 | 0.26 | |
q-SW-3-2 | 6 | 3.19 | 0.05 | 12.21 | 0.31 | q-SW-14-2 | 6 | 192.85 | 2.28 | 19.05 | 0.41 | |
q-SW-3-3 | 5 | 307.65 | 4.26 | 18.50 | 0.37 | q-SW-14-3 | 2 | 63.12 | 0.69 | - | - | |
q-SW-3-4 | 4 | - | - | 4.81 | 0.14 | q-SW-14-4 | 2 | - | - | 2.26 | 0.05 | |
q-SW-4-1 | 6 | 19.08 | 0.24 | 5.81 | 0.21 | q-SW-15-1 | 6 | 34.07 | 0.41 | 7.51 | 0.24 | |
q-SW-4-2 | 5 | 14.91 | 0.18 | 10.54 | 0.26 | q-SW-15-2 | 6 | 40.33 | 0.48 | 15.05 | 0.35 | |
q-SW-4-3 | 2 | 307.65 | 10.56 | - | - | q-SW-16-1 | 3 | 213.17 | 2.49 | 3.98 | 0.10 | |
q-SW-4-4 | 6 | 59.53 | 0.70 | 12.31 | 0.31 | q-SW-16-2 | 4 | - | - | 11.03 | 0.23 | |
q-SW-6-1 | 2 | 35.63 | 0.38 | 3.29 | 0.06 | q-SW-16-3 | 2 | 2.74 | 0.02 | 2.41 | 0.05 | |
q-SW-6-2 | 6 | 8.46 | 0.11 | 8.63 | 0.26 | q-SW-16-4 | 5 | 20.46 | 0.24 | 14.44 | 0.31 | |
q-SW-6-3 | 2 | 2.61 | 0.02 | 2.41 | 0.05 | q-SW-16-5 | 7 | 29.99 | 0.37 | 19.95 | 0.45 | |
q-SW-6-4 | 7 | 29.03 | 0.36 | 23.57 | 0.50 | q-SW-17-1 | 5 | 53.76 | 0.62 | 7.77 | 0.21 | |
q-SW-6-5 | 8 | 7.57 | 0.12 | 6.58 | 0.27 | q-SW-17-2 | 5 | 2.98 | 0.04 | 26.98 | 0.48 | |
q-SW-6-6 | 3 | 35.92 | 0.40 | 3.54 | 0.09 | q-SW-18-1 | 5 | 145.14 | 1.69 | 4.18 | 0.16 | |
q-SW-6-7 | 4 | 49.75 | 0.56 | 8.91 | 0.20 | q-SW-18-2 | 2 | - | - | 2.29 | 0.05 | |
q-SW-7-1 | 5 | 12.92 | 0.16 | 15.52 | 0.33 | q-SW-18-3 | 6 | 262.05 | 3.16 | 31.38 | 0.57 | |
q-SW-7-2 | 2 | 147.28 | 1.66 | 2.36 | 0.05 | q-SW-18-4 | 7 | 17.23 | 0.22 | 13.01 | 0.35 | |
q-SW-7-3 | 6 | 11.66 | 0.15 | 10.25 | 0.28 | q-SW-18-5 | 2 | - | - | 5.50 | 0.09 | |
q-SW-8-1 | 2 | - | - | 4.40 | 0.08 | q-SW-18-6 | 4 | 200.62 | 2.35 | 10.23 | 0.22 | |
q-SW-8-2 | 3 | 90.82 | 1.02 | 4.07 | 0.10 | q-SW-18-7 | 5 | 228.35 | 2.71 | 88.81 | 1.24 | |
q-SW-8-3 | 2 | - | - | - | - | q-SW-19-1 | 8 | 15.85 | 0.21 | 10.59 | 0.32 | |
q-SW-8-4 | 2 | 45.35 | 0.49 | - | - | q-SW-19-2 | 7 | 178.86 | 2.12 | 14.09 | 0.37 | |
q-SW-8-5 | 4 | 114.44 | 1.31 | 8.39 | 0.19 | q-SW-19-3 | 7 | 54.88 | 0.64 | 16.95 | 0.38 | |
q-SW-9-1 | 2 | - | - | 2.12 | 0.05 | q-SW-19-4 | 6 | 74.96 | 0.87 | 11.80 | 0.30 | |
q-SW-9-2 | 6 | 8.40 | 0.11 | 10.50 | 0.28 | q-SW-19-5 | 5 | 23.13 | 0.27 | 5.86 | 0.18 | |
q-SW-9-3 | 2 | 24.99 | 0.26 | 4.68 | 0.08 | q-SW-20-1 | 8 | 307.65 | 5.77 | 55.70 | 0.97 | |
q-SW-9-4 | 6 | 59.00 | 0.69 | 17.45 | 0.39 | q-SW-20-2 | 5 | 34.46 | 0.40 | 13.88 | 0.30 | |
q-SW-9-5 | 6 | 95.80 | 1.11 | 14.16 | 0.34 | LC-QTL | 83 | 18 | 52.15 | |||
q-SW-10-1 | 5 | 6.28 | 0.08 | 3.34 | 0.14 | SC-QTL | 205 | 43 | 13.25 | |||
q-SW-10-2 | 2 | 307.65 | 4.35 | 7.36 | 0.11 | 总Total | 328 | 61 | 65.40 | 68 | 17.46 | |
q-SW-10-3 | 2 | 89.96 | 0.99 | - | - |
表4
百粒重性状相关大效应QTL和候选基因"
QTL | R2 (%) | 候选基因 Candidate gene | 基因本体生物学过程 Gene ontology biological process |
---|---|---|---|
q-SW-3-3 | 4.43 | Glyma03g31790 | 囊泡介导的运输Vesicle-mediated transport |
Glyma03g31810 | 线粒体mRNA修饰Mitochondrial mRNA modification | ||
Glyma03g31820 | 微管细胞骨架组织Microtubule cytoskeleton organization | ||
Glyma03g31940 | 甲壳素响应Response to chitin | ||
Glyma03g32040 | 高尔基体内囊泡介导转运Intra-Golgi vesicle-mediated transport | ||
q-SW-4-3 | 10.93 | Glyma04g38830 | 细胞分裂素代谢Cytokinin metabolic |
Glyma04g38870 | 甲基转移酶活性Methyltransferase activity | ||
Glyma04g38955 | 糖介导的信号通路Sugar mediated signaling pathway | ||
q-SW-8-5 | 1.36 | Glyma08g44800 | RRNA加工RRNA processing |
Glyma08g44820 | 蛋白水解Proteolysis | ||
Glyma08g44960 | 未知Unknown | ||
Glyma08g44921 | 跨膜运输Transmembrane transport | ||
q-SW-9-5 | 1.16 | Glyma09g41070 | 液泡运输Vacuolar transport |
Glyma09g41140 | 肌醇六磷酸磷酸酯的生物合成过程Myo-inositol hexakisphosphate biosynthetic process | ||
Glyma09g41150 | 胚胎发育以种子休眠结束Embryo development ending in seed dormancy | ||
Glyma09g41260 | 氧化应激响应Response to oxidative stress | ||
Glyma09g41320 | 鸟嘌呤运输Guanine transport | ||
Glyma09g41121 | 未知Unknown | ||
q-SW-13-1 | 1.83 | Glyma13g08170 | 翻译调控Regulation of translation |
q-SW-13-4 | 1.21 | Glyma13g29011 | 种子萌发Seed germination |
q-SW-14-2 | 2.37 | Glyma14g08040 | 嘧啶核糖核苷酸生物合成Pyrimidine ribonucleotide biosynthetic |
Glyma14g08050 | 缺氧响应Response to hypoxia | ||
Glyma14g08070 | 种子萌发正调控Positive regulation of seed germination | ||
Glyma14g08220 | 脱落酸应激响应Response to abscisic acid stimulus | ||
Glyma14g08075 | 未知Unknown | ||
Glyma14g08145 | 未知Unknown | ||
q-SW-16-1 | 2.58 | Glyma16g06320 | 未知Unknown |
q-SW-18-1 | 1.75 | Glyma18g10460 | 新陈代谢Metabolic |
Glyma18g10470 | 防御反应Defense response | ||
q-SW-18-3 | 3.28 | Glyma18g16720 | 蛋白质折叠Protein folding |
Glyma18g16761 | 蛋白水解Proteolysis | ||
q-SW-18-6 | 2.44 | Glyma18g36455 | 未知Unknown |
q-SW-18-7 | 2.81 | Glyma18g52250 | 盐胁迫响应Response to salt stress |
Glyma18g52260 | 转录调控Regulation of transcription | ||
Glyma18g52290 | 碳水化合物代谢Carbohydrate metabolic | ||
Glyma18g52350 | Basipetal生长素运输Basipetal auxin transport |
表5
百粒重QTL-等位变异在熟期组间的变化"
QTL | a1 | a2 | a3 | a4 | a5 | a6 | a7 | a8 | QTL | a1 | a2 | a3 | a4 | a5 | a6 | a7 | a8 | QTL | a1 | a2 | a3 | a4 | a5 | a6 | a7 | a8 | |||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1-1 | yz | 7-3 | X | yz | 14-4 | yz | |||||||||||||||||||||||||||||||||
1-2 | y | 8-1 | z | 15-1 | X | ||||||||||||||||||||||||||||||||||
1-3 | yz | 8-2 | z | 15-2 | z | z | |||||||||||||||||||||||||||||||||
2-1 | z | z | 8-3 | XYZ | yz | XZ | 16-1 | ||||||||||||||||||||||||||||||||
2-2 | z | yz | 8-4 | xyz | XYZ | XYZ | XYZ | XYZ | xyz | 16-2 | XY | yz | |||||||||||||||||||||||||||
2-3 | X | XY | z | 8-5 | xyz | xyz | xyz | xyz | 16-3 | ||||||||||||||||||||||||||||||
2-4 | XZ | 9-1 | z | 16-4 | yz | ||||||||||||||||||||||||||||||||||
2-5 | z | 9-2 | xy | z | 16-5 | yz | z | ||||||||||||||||||||||||||||||||
2-6 | yz | 9-3 | XY | 17-1 | XY | z | |||||||||||||||||||||||||||||||||
3-1 | XY | XYZ | Y | 9-4 | XYZ | y | z | 17-2 | z | y | |||||||||||||||||||||||||||||
3-2 | X | XZ | 9-5 | yz | 18-1 | XYZ | y | z | |||||||||||||||||||||||||||||||
3-3 | yz | yz | 10-1 | X | XY | 18-2 | z | ||||||||||||||||||||||||||||||||
3-4 | z | y | 10-2 | X | 18-3 | y | z | z | yz | ||||||||||||||||||||||||||||||
4-1 | yz | yz | yz | z | 10-3 | z | 18-4 | yz | yz | yz | XY | ||||||||||||||||||||||||||||
4-2 | z | yz | yz | 12-1 | 18-5 | yz | |||||||||||||||||||||||||||||||||
4-3 | z | 12-2 | z | XZ | yz | z | z | yz | 18-6 | yz | yz | y | |||||||||||||||||||||||||||
4-4 | YZ | yz | xz | z | z | 12-3 | yz | z | 18-7 | z | |||||||||||||||||||||||||||||
6-1 | 12-4 | yz | 19-1 | X | |||||||||||||||||||||||||||||||||||
6-2 | z | X | 12-5 | z | 19-2 | z | xyz | z | |||||||||||||||||||||||||||||||
6-3 | XZ | 13-1 | z | yz | z | 19-3 | XY | XY | |||||||||||||||||||||||||||||||
6-4 | z | yz | z | 13-2 | z | yz | XZ | z | 19-4 | yz | yz | z | YZ | ||||||||||||||||||||||||||
6-5 | yz | y | yz | y | yz | 13-3 | z | XYZ | z | 19-5 | z | ||||||||||||||||||||||||||||
6-6 | yz | yz | 13-4 | z | yz | 20-1 | XZ | X | z | y | yz | XY | X | ||||||||||||||||||||||||||
6-7 | xyz | 14-1 | yz | z | z | 20-2 | y | y | |||||||||||||||||||||||||||||||
7-1 | XYZ | z | 14-2 | XYZ | XY | yz | |||||||||||||||||||||||||||||||||
7-2 | 14-3 | xy | |||||||||||||||||||||||||||||||||||||
熟期组 Maturity group | 等位变异总数 Total allele | 继承等位变异 Inherent allele | 变化等位变异 Changed allele | 新生等位变异 Emerged allele | 汰除等位变异 Excluded allele | ||||||||||||||||||||||||||||||||||
Allele no. | QTL no. | Allele no. | QTL no. | Allele no. | QTL no. | Allele no. | QTL no. | Allele no. | QTL no. | ||||||||||||||||||||||||||||||
Ⅰ+Ⅱ | 292 (147, 145) | 76 | |||||||||||||||||||||||||||||||||||||
0 vs.Ⅰ+Ⅱ | 321 (162, 159) | 76 | 287 (144, 143) | 76 | 39 (21,18) | 30 | 34 (18,16) | 25 | 5 (3,2) | 5 | |||||||||||||||||||||||||||||
00 vs. 0 | 250 (125,125) | 76 | 247 (123, 124) | 76 | 77(41,36) | 49 | 3 (2,1) | 2 | 74 (39,35) | 49 | |||||||||||||||||||||||||||||
000 vs. 00 | 208 (105,103) | 76 | 189 (96,93) | 76 | 80(38,42) | 52 | 19 (9,10) | 17 | 61(29,32) | 44 | |||||||||||||||||||||||||||||
0+00+000 vs.Ⅰ+Ⅱ | 324 (163, 161) | 76 | 288 (144, 144) | 76 | 40 (22,18) | 31 | 36 (19,17) | 27 | 4(3,1) | 4 |
[1] |
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