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作物学报

作物学报 ›› 2022, Vol. 48 ›› Issue (5): 1091-1102.doi: 10.3724/SP.J.1006.2022.14063

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

栽培大豆×半野生大豆高密度遗传图谱构建及株高QTL定位

于春淼1,3(), 张勇2, 王好让3, 杨兴勇2, 董全中2, 薛红2, 张明明2, 李微微2, 王磊2, 胡凯凤2, 谷勇哲3, 邱丽娟1,3,*()   

  1. 1东北农业大学农学院, 黑龙江哈尔滨 150030
    2黑龙江省农业科学院克山分院, 黑龙江齐齐哈尔 161606
    3农作物基因资源与遗传改良国家重大科学工程 / 农业农村部种质资源利用重点实验室 / 中国农业科学院作物科学研究所, 北京 100081
  • 收稿日期:2021-04-16 接受日期:2021-09-09 出版日期:2022-05-12 网络出版日期:2021-10-18
  • 通讯作者: 邱丽娟
  • 作者简介:于春淼, E-mail: 17709858735@163.com第一联系人：**同等贡献
  • 基金资助:
    国家自然科学基金项目(31601326);中央级公益性科研院所基本科研业务费专项(S2021ZD02);中国农业科学院科技创新工程;大豆种质资源保护与利用项目资助(2019NWB036-05)

Construction of a high density genetic map between cultivated and semi-wild soybeans and identification of QTLs for plant height

YU Chun-Miao1,3(), ZHANG Yong2, WANG Hao-Rang3, YANG Xing-Yong2, DONG Quan-Zhong2, XUE Hong2, ZHANG Ming-Ming2, LI Wei-Wei2, WANG Lei2, HU Kai-Feng2, GU Yong-Zhe3, QIU Li-Juan1,3,*()   

  1. 1College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China
    2Keshan Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar 161606, Heilongjiang, China
    3National Key Facility for Gene Resources and Genetic Improvement / Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
  • Received:2021-04-16 Accepted:2021-09-09 Published:2022-05-12 Published online:2021-10-18
  • Contact: QIU Li-Juan
  • About author:First author contact:**Contributed equally to this work
  • Supported by:
    National Natural Science Foundation of China(31601326);Central Public-interest Scientific Institution Basal Research Fund(S2021ZD02);Agricultural Science and Technology Innovation Program of Chinese Academy of Agricultural Sciences;Protection and Utilization of Soybean Germplasm Resources(2019NWB036-05)

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摘要：

采用中SNP160K芯片对丰收24×通交83-611 F2群体252个植株及其亲本进行基因分型, 构建了一张由5861个SNP标记组成的全长为3661.46 cM的高密度遗传连锁图谱。利用完备区间作图法(ICIM)定位到7个株高QTL, 每个QTL可解释2.56%~10.41%的株高变异。qPH-6-1具有最高的表型变异贡献率和显性效应, 可解释10.41%的株高变异, 加性效应和显性效应分别为-1.72和18.94; qPH-18-1贡献率次之, 可解释9.64%的株高变异, 但具有最高的加性效应, 达-12.42。在F2群体中筛选出11个qPH-6-1和qPH-18-1基因型为Q6Q6/Q18Q18的单株, 平均株高167.00 cm; 筛选出16个基因型为q6q6/q18q18的植株, 平均株高为91.25 cm。在qPH-18-1定位区间内外增加23个SNP标记, 将定位区间由766.97 kb缩小至66.03 kb, 包含8个基因, 结合基因注释和相对表达量差异分析, 推测Glyma.18G279800和Glyma.18G280200可能与大豆的株高相关。本研究为大豆株型的改良提供了分子参考依据和遗传基础。

关键词: 大豆, 株高, SNP, 遗传图谱, QTL定位, 候选基因

Abstract:

In this study, 252 plants and their parents of Fengshou 24 × Tongjiao 83-611 were genotyped by SNP160K DNA-chip. A high-density genetic linkage map with a total length of 3661.46 cM was constructed, composing of 5861 SNP markers. Seven QTLs of plant height were detected by inclusive composite interval mapping (ICIM), and each one explained 2.56%-10.41% of the variation in plant height. qPH-6-1 had the highest contribution rate of phenotypic variation and dominant effect, explaining 10.41% of plant height variation, and the additive and dominant effects are -1.72 and 18.94, respectively. The contribution rate of qPH-18-1 was the second, explaining 9.64% of plant height variation, but qPH-18-1 has the highest additive effect, reaching -12.42. 11 plants with qPH-6-1 and qPH-18-1 genotypes Q6Q6/Q18Q18 were screened in F2 population with an average plant height of 167.00 cm, and 16 plants with 2-locus genotypes q6q6/q18q18 were screened out with an average plant height of 91.25 cm. The addition of 23 SNP markers inside and outside the qPH-18-1 locus interval narrowed the locus interval from 766.97 kb to 66.03 kb, containing eight genes. Combined with gene annotation and relative expression difference analysis, it was hypothesized that Glyma.18G279800 and Glyma.18G280200 might be associated with plant height of soybean. This study provides a molecular reference base and genetic basis for the improvement of soybean plant architecture.

Key words: soybean, plant height, SNP, genetic linkage map, QTLs mapping, candidate gene

表1

候选基因和内参基因表达引物序列"

引物名称
Primer name		 基因编号
Gene ID		 上游引物
Forward primer (5'-3')		 下游引物
Reverse primer (5'-3')		 产物长度
Product length (bp)
Fbox Glyma.12G051100 CTAATGGCAATTGCAGCTCTC AGATAGGGAAATTGTGCAGGT 93
Q2795 Glyma.18G279500 GTAGCAGCCATGGAAGCGATAC AGATTTGTCTCGGTGGGGAAC 122
Q2796 Glyma.18G279600 CTGCTGGCTATGATGCACAGTCA AGGTTCATATCCACCTCCACTACG 122
Q2797 Glyma.18G279700 TACATGCGTGGTTCGCCTTGC TGTATGTTAGAGGGTGGGGAAAGG 135
Q2798 Glyma.18G279800 CCTTGATGAGCCAGATGAGAAATG CATAGTACATGGTTAAGTCAGGAAC 170
Q2799 Glyma.18G279900 CATCACCACCACAAGTAGTTTGG GATTTTGAGAGTTCATTGGAACTG 132
Q2800 Glyma.18G280000 GATCCTCTCCAGAAACATTGAGATG GGGTTATTATGTGGCTCTACTTGTG 128
Q2802 Glyma.18G280200 GTACATGCAAGGACCCTCTTGG TCACTGCTCTAACACACTGGCG 124

表2

鉴定qPH-18-1基因型所用SSR标记"

标记名称
Marker name		 上游引物
Forward sequence (5'-3')		 下游引物
Reverse sequence (5'-3')		 物理位置
Physical position (bp)
BARCSOYSSR_18_1842 TGAAATGGAGGAGAAAATGGA GTCCGGGGAAACTGAACC 56,015,746-56,015,789
BARCSOYSSR_18_1843 TCGTTCGCAAAGAAAAATCC TTGGCAACAATGGAGTCTCA 56,035,543-56,035,596
BARCSOYSSR_18_1844 TGCAAGGCATTGATCTGATT AGAGGCGTCCTTCTGTTGTT 56,063,881-56,063,916
BARCSOYSSR_18_1845 TCATTGAGCCGAATCTTTTAAT CGTGCACATGGTGAGACATA 56,066,436-56,066,463
BARCSOYSSR_18_1846 CTTTTAACGATTGGGTTGGG CTTCGGCCTTAGACTTTTCG 56,068,160-56,068,221
BARCSOYSSR_18_1848 CGGTGTTGCTGACTATTGTCCT GGCTTTTGTAAACTGCTGGC 56,110,310-56,110,343
BARCSOYSSR_18_1849 TCTCGTCCCCGTATAAGGCT GGCGGATTGGAGAGAACATA 56,110,482-56,110,503
BARCSOYSSR_18_1850 AAATGCATTCGTGGCTTTCT TGGGTATTATTTGGCAAGCAC 56,138,357-56,138,410

图1

F2群体单株株高的表型分布"

表3

亲本及F2群体株高的统计分析"

性状
Trait		 亲本Parent 群体Population
丰收24
Fengshou 24		 通交83-611
Tongjiao 83-611		 幅度
Range		 均值
Mean		 标准差
SD		 峰度
Kurtosis		 偏度
Skewness
株高Plant height (cm) 90.67±3.67 191.17±6.91 60.00-230.00 144.28 30.65 0.36 -0.54

图2

大豆遗传连锁图谱中5861个SNP标记的分布 图中黑色横线表示标记位置; 图中颜色表示标记密度, 由红到蓝色渐变表示标记密度由大到小。"

表4

SNP标记在构建的遗传图谱中分布"

染色体号
Chromosome-ID		 标记数量
Number of markers		 总图距
Total distance (cM)		 平均图矩
Average distance (cM)
1 277 170.23 0.61
2 338 220.66 0.65
3 344 158.81 0.46
4 379 195.95 0.52
5 312 176.98 0.57
6 310 209.66 0.68
7 236 170.11 0.72
8 250 203.31 0.81
9 304 192.14 0.63
10 354 200.50 0.57
11 268 195.60 0.73
12 150 118.50 0.79
13 261 227.96 0.87
14 276 152.34 0.55
15 272 162.66 0.60
16 244 177.84 0.73
17 455 185.47 0.41
18 285 195.06 0.68
19 240 177.67 0.74
20 306 170.02 0.56
合计Total 5861 3661.46 0.62

表5

完备区间作图法定位的大豆株高QTL"

QTL 染色体
Chr.		 标记区间
Marker flanking		 位置
Position (cM)		 区间长度
Length
(cM)		 LOD 贡献率
PVE (%)		 加性效应
Add		 显性效应
Dmo		 已报道位点
Reported
qPH-6-1 6 Gm06_18957454-Gm06_17916496 57 3.00 9.24 10.41 -1.72 18.94 Rossi et al., 2013[4]
qPH-8-1 8 Gm08_9294990-Gm08_9210707 143 10.00 2.57 2.56 2.45 -9.12 —
qPH-10-1 10 Gm10_8606306-Gm10_7981987 134 7.00 3.00 2.95 4.30 -8.25 —
qPH-13-1 13 Gm13_38753560-Gm13_37989992 56 6.00 4.16 4.73 -9.04 3.38 Pathan et al., 2013[25]
qPH-13-2 13 Gm13_28621502-Gm13_28455484 115 3.00 2.70 2.67 -2.20 9.56 Li et al., 2009[26]
qPH-18-1 18 Gm18_56044812-Gm18_56811782 16 6.00 8.58 9.64 -12.42 1.84 Kim et al., 2012[12]
qPH-20-1 20 Gm20_33777405-Gm20_33894103 56 1.00 3.77 4.05 -8.10 -1.49 Chapman et al., 2003[27]

表6

聚合不同基因型株高QTL对株高的影响"

聚合纯合提升株高基因型的QTL
QTL of polymerized homozygous genotypes with increase plant height		 聚合纯合降低株高基因型的QTL
QTL of polymerized homozygous genotypes with reduce plant height
位点数
No. of QTL		 植株数量
No. of plants		 平均株高
Average height (cm)		 分组
Group		 P值
P-value		 位点数
No. of QTL		 植株数量
No. of plants		 平均株高
Average height (cm)		 分组
Group		 P值
P-value
0 36 131.39±4.48 AC 对照Control 0 35 170.86±3.30 a 对照Control
1 64 139.45±3.89 AB 0.548 1 61 154.18±3.19 b 0.013*
2 74 146.49±3.28 BD 0.043* 2 70 137.14±3.18 c 0.000*
3 26 154.23±4.78 DE 0.010* 3 33 125.00±4.99 d 0.000*
4 15 166.67±5.66 E 0.000* 4 15 133.00±7.49 cd 0.000*
5 3 160.00±10.00 — — 5 4 115.00±10.41 cd 0.000*

图3

使用丰收24和通交83-611 F2群体定位到的新qPH-18-1"

表7

定位区间内基因注释及同源基因"

基因编号
Gene ID		 基因注释
Gene annotation		 同源基因
Homologous gene
Glyma.18G279500 后期促进复合物3 (APC3, CDC27)
Anaphase-promoting complex subunit 3 (APC3, CDC27)		 Phvul.008G021500
AT2G20000
Glyma.18G279600 — —
Glyma.18G279700 — —
Glyma.18G279800 在Pmr5和Cas1p中发现的GDSL/SGNH类酰基酯酶家族(PC-酯酶)
GDSL/SGNH-like Acyl-Esterase family found in Pmr5 and Cas1p (PC-Esterase);
PMR5 N terminal Domain (PMR5N)		 Phvul.008G021200
AT5G15900
Glyma.18G279900 在Pmr5和Cas1p中发现的GDSL/SGNH类酰基酯酶家族(PC-酯酶)
GDSL/SGNH-like Acyl-Esterase family found in Pmr5 and Cas1p (PC-Esterase);
PMR5 N terminal Domain (PMR5N)		 Phvul.008G021100
Glyma.18G280000 — —
Glyma.18G280100 与F27J15.22相关; 油质蛋白
F27J15.22-RELATED; Oleosin		 —
Glyma.18G280200 富脯氨酸受体样蛋白激酶perk8
Proline-rich receptor-like protein kinase perk8		 AL7G52030

图4

群体中植株基因型与表型相关性分析 *、**和***分别表示在0.05、0.01和0.001水平差异显著。方形柱上下边框分别表示上下四分位数所在位置, 中部黑线为该组数据的中位数。"

图5

区间内基因的组织表达模式和表达分析"

表8

使用SNP芯片检测标记构建的遗传图谱比较"

芯片名称
SNP-chip name		 亲本间SNP数
No. of parental SNPs		 图谱标记数
No. of markers		 图谱总长
Total distance (cM)		 标记间平均距离
Average distance (cM)
BARCSoySNP6K 1133-2585 1063-2283 1908.7-2834 1.10-1.80
SoyaSNP180K 23,429-28,385 1570-8967 3454-5050 0.50-2.2
SNP160K 48,248 5861 3661.46 0.62
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