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作物杂志,2021, 第3期: 8–18 doi: 10.16035/j.issn.1001-7283.2021.03.002

• 遗传育种·种质资源·生物技术 • 上一篇    下一篇

大豆百粒重相关基因的全基因组发掘分析

宿洋1(), 杨静2, 郭勇2(), 杜维俊1(), 邱丽娟2()   

  1. 1山西农业大学农学院,030801,山西晋中
    2中国农业科学院作物科学研究所/农作物基因资源与遗传改良国家重大科学工程/农业农村部北京大豆生物学重点实验室,100081,北京
  • 收稿日期:2021-04-29 修回日期:2021-05-11 出版日期:2021-06-15 发布日期:2021-06-22
  • 通讯作者: 郭勇,杜维俊,邱丽娟
  • 作者简介:宿洋,主要从事大豆基因发掘研究,E-mail： sxhq2275@163.com
  • 基金资助:
    国家自然科学基金(31871651);山西农业大学育种工程项目(YZGC096);山西省自然科学基金(201801D121247)

Whole Genome Discovery and Analysis of Genes Related to 100-Seed Weight in Soybean

Su Yang1(), Yang Jing2, Guo Yong2(), Du Weijun1(), Qiu Lijuan2()   

  1. 1College of Agriculture, Shanxi Agricultural University, Jinzhong 030801, Shanxi, China
    2Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/The National Key Facility for Crop Gene Resources and Genetic Improvement/MOA Key Laboratory of Soybean Biology (Beijing), Beijing 100081, China
  • Received:2021-04-29 Revised:2021-05-11 Online:2021-06-15 Published:2021-06-22
  • Contact: Guo Yong,Du Weijun,Qiu Lijuan

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摘要：

百粒重是大豆重要的产量性状之一,利用正向和反向遗传学方法鉴定与籽粒大小/粒重相关的基因具有重要的理论和实践意义。利用拟南芥和水稻等模式植物中已明确功能的调控籽粒大小/粒重的基因,基于序列相似和结构域相同的原则,在大豆全基因组内筛选到175个同源基因,通过基因表达谱分析发现有22个基因在大豆种子中特异性表达。利用56份大豆种质资源重测序数据查找这些基因内的SNP位点,共得到2769个SNP位点,从中筛选得到在野生大豆和栽培大豆中分化明显的SNP位点121个。通过扩增测序对其中的16个导致非同义变异的SNP位点进行验证,发现有5个SNP位点在野生大豆中为一种变异,而在栽培大豆中为另一种变异。利用2368份大豆种质资源的重测序数据获得了其中的4个SNP位点的变异数据,结合其中1695份材料的百粒重表型分析,发现每个SNP位点对应的野生和突变基因型材料的百粒重表型间都存在极显著差异,并且每个SNP位点中野生基因型材料的百粒重大部分≥12g,突变基因型材料的百粒重大部分＜12g,因此上述4个SNP位点所在的基因（Glyma.05G019800、Glyma.07G022800、Glyma.13G259700和Glyma.13G261700）可能与大豆籽粒大小/粒重的调控有关。获得了与大豆百粒重相关的4个候选基因,为大豆百粒重QTL的精细定位和功能标记的开发以及调控大豆籽粒大小/粒重的基因的功能研究提供了参考。

关键词: 大豆, 百粒重, 同源基因, SNP, 重测序

Abstract:

100-seed weight is an important trait related to yield in soybean breeding. Therefore, identification of genes related to seed size/weight by using forward and reverse genetic methods had important theoretical and practical significance. Functional genes regulating seed size/weight in Arabidopsis thaliana and rice had been obtained from published literatures and a total of 175 homologous genes were identified from whole soybean genome based on the principle of sequence similarity and domain identity. Gene expression profile analysis showed that 22 genes were specifically expressed in soybean seeds. Using the resequencing data of 56 germplasm resources, a total of 2769 SNPs were identified in these genes and 121 SNPs had co-relationship between wild and cultivated soybean. Sixteen SNPs with non-synonymous variations were verified by PCR based sequencing in 26 soybean accessions and the results showed that five SNPs was related to seed size, and had the different variations in wild and cultivated soybean. The genotypes of four SNPs were obtained from the resequencing data of 2368 soybean accessions and genotype-phenotype association analysis suggested that there was a very significant difference in 100-seed weight phenotype between accessions with wild type and mutant variations corresponding to each SNP. The 100-seed weight of majority accessions with WT-genotype was more than 12g while that of accessions with Mut-genotype was less than 12g. Therefore, the four genes harboring these four SNPs may be related to the regulation of soybean seed size/weight. Four candidate genes related to 100-seed weight were obtained in soybean, which provided a reference for fine mapping and functional marker development of soybean 100-seed weight and the functional study of genes regulating soybean seed size/weight.

Key words: Soybean, 100-seed weight, Homologous gene, SNP, Resequencing

表1

调控植物籽粒大小/粒重的功能基因

基因名称
Gene name		 物种
Species		 基因编号
Gene ID		 生物学功能
Biological function		 大豆中基因拷贝数
Copy number in soybean		 参考文献
Reference
激素信号转导Hormone signal transduction
KLU Arabidopsis AT1G13710 Cytochrome P450 5 [20]
SOB7 Arabidopsis AT1G17060 Cytochrome p450 72C1 13 [21]
AHK3 Arabidopsis AT1G27320 Histidine kinase 3 2 [20]
CKX5 Arabidopsis AT1G75450 Cytokinin oxidase 5 2 [22]
AHK4 Arabidopsis AT2G01830 Histidine kinase: cytokinin-binding receptor 5 [20]
DET2 Arabidopsis AT2G38050 Brassinolide biosynthetic 2 [20]
CKX1 Arabidopsis AT2G41510 Cytokinin oxidase/dehydrogenase 1 2 [22]
EOD3 Arabidopsis AT2G46660 Cytochrome P450 3 [21]
DWF4 Arabidopsis AT3G50660 Cytochrome P450 superfamily protein 3 [5]
CYP78A9 Arabidopsis AT3G61880 Cytochrome P450 78a9 3 [21]
AP2 Arabidopsis AT4G36920 Integrase-type DNA-binding superfamily protein 4 [7]
ATMYB56 Arabidopsis AT5G17800 Myb domain protein 56 2 [22]
AGG3 Arabidopsis AT5G20635 Atypical heterotrimeric G-protein gamma-subunit 4 [23]
AHK2 Arabidopsis AT5G35750 Histidine kinase AHK2 2 [20]
ABA2 Arabidopsis AT1G52340 Xanthoxin dehydrogenase 2 [21]
ABI5 Arabidopsis AT2G36270 Basic-leucine zipper (bZIP) transcription factor family protein 3 [21]
BRI1 Arabidopsis AT4G39400 Protein BRASSINOSTEROID INSENSITIVE 1 2 [21]
ARF2 Arabidopsis AT5G62000 Auxin response factor 2 4 [5]
DWARF 61 Rice OS01G0718300 Receptor serine/threonine kinase 2 [23]
OsBZR1 Rice OS07G0580500 Brassinosteroid (BR) regulated growth response 6 [21]
GSK2 Rice OS05G0207500 GSK3/SHAGGY-like kinase 1 [21]
BG1 Rice Os03g0175800 Positive regulator of auxin response and transport 1 [21]
DWARF 11 Rice OS04G0469800 Brassinosteroid (BR) biosynthesis 1 [21]
GE Rice OS07G0603700 Cytochrome P450 78A5 5 [23]
泛素代谢途径Ubiquitin pathway
GW2 Rice OS02G0244100 RING-type E3 ubiquitin ligase 2 [8]
UBP15 Arabidopsis AT1G17110 Ubiquitin-specific protease 15 2 [24]
DA1 Arabidopsis AT1G19270 Ubiquitin receptors 2 [25]
DA2 Arabidopsis AT1G78420 E3 ubiquitin-protein ligase DA2 2 [26]
EOD1 Arabidopsis AT3G63530 E3 ubiquitin ligase 2 [21]
DAR1 Arabidopsis AT4G36860 Ubiquitin binding protein 6 [23]
其他Others
SAMBA Arabidopsis AT1G32310 Valine-tRNA ligase 2 [23]
MINI3 Arabidopsis AT1G55600 Member of WRKY Transcription Factor 2 [2]
IKU1 Arabidopsis AT2G35230 VQ motif-containing protein 5 [20]
TTG2 Arabidopsis AT2G37260 WRKY family transcription factor 2 [20]
SOD7 Arabidopsis AT3G11580 AP2/B3-like transcriptional factor 4 [21]
IKU2 Arabidopsis AT3G19700 Leucine-rich repeat protein kinase 1 [20]
FER Arabidopsis AT3G51550 Malectin/receptor-like protein kinase 2 [21]
STK Arabidopsis AT4G09960 MADS box transcription factor 2 [22]
基因名称
Gene name		 物种
Species		 基因编号
Gene ID		 生物学功能
Biological function		 大豆中基因拷贝数
Copy number in soybean		 参考文献
Reference
RPT2A Arabidopsis AT4G29040 Regulatory particle AAA-ATPase 2A 4 [23]
ANT Arabidopsis AT4G37750 Integrase-type DNA-binding superfamily protein 8 [20]
DPA4 Arabidopsis AT5G06250 AP2/B3-like transcriptional factor 4 [21]
MET1 Arabidopsis AT5G49160 Methyltransferase 1 2 [23]
AGL62 Arabidopsis AT5G60440 AGAMOUS-like 62 24 [20]
SHB1 Arabidopsis At4G25350 Acts in cryptochrome signaling 1 [20]
GS2 Rice Os02G0701300 Growth-regulating factor 4-like 1 [21]
SMG1 Rice OS02G0787300 Mitogen-activated protein kinase kinase 5 2 [23]
GS3 Rice OS03G0407400 Keratin-associated protein 5-5 4 [21]
qGL3 Rice Os03G0646900 Serine/threonine phosphatase 1 [21]
RGB1 Rice OS03G0669100 Deoxyuridine 5'-triphosphate nucleotidohydrolase-like 2 [23]
OsGIF1 Rice OS03G0733600 GRF1-interacting factor 1 4 [23]
GS5 Rice OS05G0158500 Serine carboxypeptidase-like 26 3 [23]
RGA1 Rice OS05G0333200 Guanine nucleotide-binding protein alpha-1 subunit 4 [23]
OsMAPK6 Rice OS06G0154500 Mitogen-activated protein kinase 1-like 2 [27]
TGW6 Rice OS06G0623700 Protein STRICTOSIDINE SYNTHASE-LIKE 10 6 [28]
GW6a Rice OS06G0650300 Probable N-acetyltransferase HLS1 2 [23]
GLW7 Rice Os07G0505200 Plant-specific transcription factor 1 [23]
GW7 Rice OS07G0603300 Protein LONGIFOLIA 1 8 [29]
GW8 Rice OS08G0531600 Squamosa promoter binding like protein 16 2 [30]
DEP1 Rice OS09G0441900 Keratin-associated protein 5-5 4 [31]

表2

大豆百粒重相关基因在染色体上的定位

染色体
Chromosome		 泛素代谢途径
Ubiquitin
pathway		 激素信号转导途径
Hormone signal
transduction		 其他
Others		 合计
Total
1 1 5 3 9
2 1 4 5 10
3 0 3 4 7
4 0 4 6 10
5 0 5 3 8
6 0 6 6 12
7 0 4 4 8
8 0 4 7 11
9 0 1 2 3
10 1 0 21 22
11 1 6 2 9
12 2 0 0 2
13 3 5 5 13
14 1 2 3 6
15 2 7 0 9
16 1 2 2 5
17 1 4 6 11
18 0 0 3 3
19 0 4 7 11
20 0 0 5 5
Scaffold 0 0 1 1
合计Total 14 66 95 175

图1

大豆百粒重相关基因的电子表达谱

表3

大豆不同组织中特异性表达的基因

植物组织
Plant tissue		 泛素代谢途径
Ubiquitin pathway		 激素信号
转导途径
Hormone signal transduction		 其他
Others		 合计
Total
种子Seed 3 6 12 21
花Flower 5 14 16 35
荚Pod 0 4 7 11
根毛Root hairs 0 2 6 8
叶片Leaf 1 5 1 7
根Root 2 5 18 25
根瘤Nodules 1 7 5 13
顶端分生组织SAM 0 17 15 32
茎Stem 2 2 7 11

表4

非同义变异SNP位点分布情况

基因号Gene ID 染色体Chromosome 区域Region 遗传分化指数Fst 参考碱基Ref 突变碱基Mutant type 氨基酸变异Amino acid variation
Glyma.02G179300 Gm02 CDS 0.45 G T T<->K
Glyma.02G194000 Gm02 CDS 0.49 T C I<->T
Glyma.05G019800 Gm05 CDS 0.52 T C S<->P
Glyma.07G022800 Gm07 CDS 0.51 T C I<->M
Glyma.07G052300 Gm07 CDS 0.56 T A S<->T
Glyma.13G055700 Gm13 CDS 0.48 T C I<->V
Glyma.13G055700 Gm13 CDS 0.47 T C T<->A
Glyma.13G055700 Gm13 CDS 0.51 C A V<->L
Glyma.13G055700 Gm13 CDS 0.62 T C N<->D
Glyma.13G259700 Gm13 CDS 0.58 C T S<->N
Glyma.13G261700 Gm13 CDS 0.69 C T S<->N
Glyma.13G262000 Gm13 CDS 0.52 T G M<->L
Glyma.13G262000 Gm13 CDS 0.57 C T G<->D
Glyma.17G080000 Gm17 CDS 0.58 C T E<->K
Glyma.17G080500 Gm17 CDS 0.65 A G I<->V
Glyma.17G080500 Gm17 CDS 0.46 A G K<->E

图2

16个SNP在26份大豆资源中的分布 W：野生大豆;C：栽培大豆。“*”代表在P < 0.05水平上差异显著

图3

不同SNP类型材料对应的百粒重表型分析 “**”代表在P < 0.01水平上差异显著

图4

不同百粒重范围内大豆资源数量分布

表5

候选基因功能注释

基因号
Gene ID		 拟南芥/水稻中同源基因
Homologous gene in Arabidopsis/rice		 功能注释
Functional annotation
Glyma.05G019800 GW7 单细胞的生长调节
Glyma.07G022800 GW6a N-乙酰基转移酶活性
Glyma.13G259700 UBP15/SOD2 泛素水解酸活性
Glyma.13G261700 SOB7 氧化还原酶活性
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