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作物学报

作物学报 ›› 2023, Vol. 49 ›› Issue (3): 719-730.doi: 10.3724/SP.J.1006.2023.14195

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

基于高密度遗传图谱的蓖麻种子大小性状QTL定位

杨俊芳1,2(), 王宙1(), 乔麟轶2, 王亚1, 赵宜婷1, 张宏斌1, 申登高1, 王宏伟3,*(), 曹越1,*()   

  1. 1山西农业大学经济作物研究所, 山西太原 030031
    2山西农业大学农学院, 山西太原 030031
    3山西农业大学社会服务部, 山西太原 030031
  • 收稿日期:2021-10-21 接受日期:2022-06-07 出版日期:2023-03-12 网络出版日期:2022-07-08
  • 通讯作者: 王宏伟,曹越
  • 作者简介:杨俊芳, E-mail: sx1987yjf@126.com
    王宙, E-mail: 419309976@qq.com第一联系人：**同等贡献
  • 基金资助:
    山西省农业科学院国家自然基金培育项目(YGJPY1904);山西省科技厅青年科学研究项目(20210302124364);山西农业大学生物育种工程项目(YZGC050)

QTL mapping of seed size traits based on a high-density genetic map in castor

YANG Jun-Fang1,2(), WANG Zhou1(), QIAO Lin-Yi2, WANG Ya1, ZHAO Yi-Ting1, ZHANG Hong-Bin1, SHEN DengGao1, WANG HongWei3,*(), CAO Yue1,*()   

  1. 1Institute of Industrial Crops, Shanxi Agricultural University, Taiyuan 030031, Shanxi, China
    2College of Agriculture, Shanxi Agricultural University, Taiyuan 030031, Shanxi, China
    3Social Service Department of Shanxi Agricultural University, Taiyuan 030031, Shanxi, China
  • Received:2021-10-21 Accepted:2022-06-07 Published:2023-03-12 Published online:2022-07-08
  • Contact: WANG HongWei,CAO Yue
  • About author:First author contact:**Contributed equally to this work
  • Supported by:
    Shanxi Academy of Agricultural Sciences for Cultivating the National Natural Science Foundation(YGJPY1904);Youth Scientific Research Project of Science and Technology Department of Shanxi Province(20210302124364);Biological Breeding Engineering of Shanxi Agricultural University(YZGC050)

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摘要：

蓖麻种子大小直接影响产量, 不同的蓖麻材料间种子大小差异较大, 深入研究蓖麻种子大小性状的遗传机制对蓖麻种子产业的发展具有重要意义。本研究以蓖麻两性自交系SL1为父本, 雌性系HCH1为母本1 (组合1)、雌性系HCH3为母本2 (组合2), 分别构建F2、BC1群体。首先, 分析2组遗传群体种子大小性状间的相关性。其次, 利用全基因组测序技术(whole genome sequencing,WGS)对组合1的F2群体中的150个单株进行测序分析, 构建高密度遗传图谱并结合种子大小性状表型数据进行数量性状座位(quantitative trait locus, QTL)定位分析。最后, 对QTL区间包含的基因进行BLAST同源比对和KEGG通路富集分析确定候选基因。结果表明, 不同组合群体的种子大小各性状间的相关性有差异, 种子的长度和宽度相关性最显著。共检测到种子大小性状相关QTL位点18个, 其中种子长度2个QTLs、种子宽度5个QTL、种子厚度4个QTL、百粒重7个QTL, 分别分布在连锁群1、4、7、8、9、10上, LOD值介于3.77~7.40, 变异贡献率介于0.71%~86.20%。基于这些分析, 筛选到6个调控蓖麻种子大小的候选基因28470.m000435、29908.m006143、29848.m004589、27752.m000045、29683.m000480和29848.m004611。本研究为蓖麻种子大小相关基因的精细定位和克隆、分子标记辅助育种及基因功能的深入研究奠定了一定的理论基础。

关键词: 蓖麻, 高密度遗传图谱, 种子大小, QTL定位, KEGG, 候选基因

Abstract:

The seed size of castor (Ricinus communis L.) directly affects the yield, and there is a great difference in seed size among different castor varieties. It is of great significance to further study the genetic mechanism of castor seed size traits for the development of castor seed industry. In this study, we used monoecious inbred lines SL1 as male parent, pistillate line HCH1 as female parent 1 (Combination 1), and pistillate line HCH3 as female parent 2 (Combination 2) to construct F2 and BC1 populations, respectively. Firstly, the correlations between seed size traits were analyzed by phenotypic statistics of the two genetic populations. Secondly, based on the phenotypic data of 150 individual plants in F2 population from Combination 1, a high-density genetic map was constructed using genotyping by whole genome sequencing technology (WGS), and QTL analysis was performed for the seed size traits. Finally, the KEGG pathway enrichment and BLAST comparison were performed to determine the candidate genes in the definite QTL region. The results showed that the correlation between seed traits was different among different combinations and populations, and the correlation between seed length and width was the most significant by the phenotypic analysis. And a total of 18 QTLs were detected for four traits including 2 QTLs for seed length, 5 QTLs for seed width, 4 QTLs for seed thickness, and 7 QTLs for hundred-grain weight, which were distributed on linkage groups 1, 4, 7, 8, 9, and 10, respectively. The LOD values ranged from 3.77 to 7.40, and the contribution of variation rate ranged from 0.71% to 86.20%. Based on these results, six candidate genes (28470.m000435, 29908.m006143, 29848.m004589, 27752.m000045, 29683.m000480, and 29848.m004611) for regulating seed size were screened. This study lays a theoretical foundation for further research on fine mapping and gene cloning, molecular marker-assisted breeding and gene function analysis of castor seed size traits.

Key words: castor, high-density genetic map, seed size, QTL mapping, KEGG, candidate gene

表1

2组亲本及后代群体种子大小性状表型统计分析"

群体
Population		 性状
Trait		 统计量
Number		 极小值
Min.		 极大值
Max.		 均值
Mean		 标准差
SD		 双侧
Sig.		 峰度
Kurtosis		 偏度
Skewness
SL1, HCH1 种子长Seed length 2 13.00 16.04 14.52 2.15 0.07 — —
种子宽Seed width 2 9.04 9.52 9.28 0.34 0.02 — —
种子厚Seed thickness 2 6.40 6.62 6.51 0.16 0.01 — —
百粒重100-grain weight 2 29.62 47.20 38.41 12.43 0.14 — —
B 种子长Seed length 217 13.09 17.22 15.13 0.82 0.00 -0.18 -0.01
种子宽Seed width 217 8.30 10.04 9.16 0.36 0.00 -0.26 -0.24
种子厚Seed thickness 217 5.40 7.31 6.39 0.30 0.00 0.28 0.21
百粒重100-grain weight 217 15.77 52.64 40.13 5.89 0.00 1.42 -0.78
D 种子长Seed length 66 12.73 16.42 14.39 0.69 0.00 0.87 -0.05
种子宽Seed width 66 8.02 9.84 9.03 0.35 0.00 0.54 -0.57
种子厚Seed thickness 66 5.70 6.71 6.35 0.21 0.00 0.04 -0.43
百粒重100-grain weight 66 24.98 43.92 37.09 4.30 0.00 0.42 -0.76
SL1, HCH3 种子长Seed length 2 13.10 16.04 14.57 2.08 0.06 — —
种子宽Seed width 2 8.80 9.52 9.16 0.51 0.02 — —
群体
Population		 性状
Trait		 统计量
Number		 极小值
Min.		 极大值
Max.		 均值
Mean		 标准差
SD		 双侧
Sig.		 峰度
Kurtosis		 偏度
Skewness
种子厚Seed thickness 2 6.40 6.62 6.51 0.16 0.01 — —
百粒重100-grain weight 2 35.02 47.20 41.11 8.61 0.09 — —
A 种子长Seed length 52 13.16 16.48 14.75 0.63 0.00 0.35 0.03
种子宽Seed width 52 8.62 10.10 9.31 0.31 0.00 -0.34 -0.15
种子厚Seed thickness 52 6.00 7.04 6.37 0.24 0.00 -0.06 0.66
百粒重100-grain weight 52 34.20 48.12 41.16 3.07 0.00 -0.45 -0.10
C 种子长Seed length 41 13.28 15.54 14.41 0.55 0.00 -0.18 -0.14
种子宽Seed width 41 8.60 9.80 9.15 0.29 0.00 -0.28 0.07
种子厚Seed thickness 41 5.02 6.60 6.27 0.27 0.00 11.96 2.81
百粒重100-grain weight 41 30.90 45.64 38.88 3.16 0.00 -0.33 -0.09

图1

测序亲本和F2代的部分种子 a: 组合1亲本, SL1为父本, HCH1为母本。b: 组合1部分F2代种子, 字母B表示F2代种子, 后面的数字为材料编号。"

图2

测序F2群体蓖麻种子大小性状表型频率分布图"

表2

2组BC1和F2群体种子大小性状相关性分析"

性状
Trait		 种子长
Seed length		 种子宽
Seed width		 种子厚
Seed thickness		 百粒重
100-grain weight
种子长Seed length 0.621** B 0.610** B 0.583** B
0.650** D 0.521** D 0.297* D
种子宽Seed width 0.386* C 0.505** B 0.558** B
0.551** A 0.381** D 0.323** D
种子厚Seed thickness 0.127 C -0.028 C 0.445** B
0.359** A 0.465** A 0.117 D
百粒重100-grain weight 0.560** C 0.453** C 0.411* C
0.086 A 0.108 A 0.006 A

表3

遗传连锁群信息统计"

连锁群
Linkage		 标记数目
Marker number		 遗传距离
Length (cM)		 平均距离
Average length (cM)		 最大间隙
Maximum gap
LG1 1949 1171.78 0.60 61.01
LG2 970 458.32 0.47 9.05
LG3 659 397.43 0.60 20.54
LG4 626 349.77 0.56 9.40
LG5 497 281.76 0.57 6.46
LG6 246 134.67 0.55 23.25
LG7 243 196.25 0.81 24.37
LG8 182 120.87 0.66 25.15
LG9 242 170.22 0.70 12.33
LG10 99 73.96 0.75 4.53
平均Average 571 335.50 0.59 —
总计Total 5713 3355.03 — —

图3

QTL定位结果 a: 种子长度定位图; b: 种子宽度定位图; c: 种子厚度定位图; d: 百粒重定位图。SL: 种子长度; SW: 种子宽度; ST: 种子厚度; HGW: 百粒重。"

表4

QTL分析结果"

性状
Trait		 染色体
Chr.		 QTL 位置
Position (cM)		 LOD值
LOD value		 加性效应Additive effect 显性效应Dominant effect 贡献率
R2 (%)		 99%置信区间
99% confidence interval
SL 1 qSL1 11.21 4.06 0.06 0.00 3.67 7.8-12.9
SL 7 qSL7 97.81 7.40 -0.02 0.00 22.16 91.2-98.9
SW 4 qSW4 169.31 3.87 0.10 -0.03 77.60 163.2-170.1
SW 7 qSW7-1 10.91 4.82 -0.05 -0.02 8.74 3.6-13.9
SW 7 qSW7-2 115.51 3.77 -0.04 0.01 11.59 107.0-119.6
SW 8 qSW8-1 96.01 4.60 -0.13 0.04 80.40 92.2-96.7
SW 8 qSW8-2 107.01 3.90 0.13 0.04 70.21 106.1-107.7
ST 4 qST4 85.51 3.87 -0.04 -0.01 23.75 83.9-88.3
ST 8 qST8-1 93.21 4.67 -0.05 0.01 86.20 90.9-96.0
ST 8 qST8-2 107.51 3.94 0.09 0.01 80.55 106.7-108.7
ST 10 qST10 71.11 5.26 -0.01 -0.01 0.71 67.5-73.0
HGW 1 qHGW1-1 3.31 4.11 -1.57 0.20 75.55 3.0-5.2
HGW 1 qHGW1-2 223.21 5.34 -1.70 0.08 30.79 223.1-236.5
HGW 1 qHGW1-3 397.91 4.30 -1.88 0.15 75.55 396.9-398.7
HGW 7 qHGW7-1 29.41 4.21 -0.27 -0.04 9.44 26.7-36.0
HGW 7 qHGW7-2 84.51 4.35 -0.26 0.13 16.60 84.1-86.2
HGW 7 qHGW7-3 97.81 4.88 -0.27 0.16 19.68 92.1-98.9
HGW 9 qHGW9 149.41 4.76 -0.23 0.26 20.05 138.2-157.3

图4

种子宽度QTL区间基因KEGG富集分析"

表5

种子大小性状候选基因"

性状位点
Trait locus		 染色体
位置Scaffords		 物理位置
Physical position (bp)		 所在基因ID
Gene ID		 拟南芥基因
Arabidopsis gene		 描述
Description
qSL7, qHGW7-3,
qHGW7-2		 29,848 962,738, 961,557,
961,387		 29848.t000167: 29848.m004611 AT4G32190.1 参与淀粉起始的蛋白质
Protein involved in starch initiation
qST4 29,908 169,970 29908.t000194: 29908.m006143 AT1G01720.1 具有NAC结构域的转录激活家族
Belongs to a large family of putative transcriptional activators with NAC domain.
qST8-1 29,683 197,190 29683.t000018: 29683.m000480 AT2G17030.1 编码SKP1/ASK互作蛋白
Encodes a SKP1/ASK-interacting protein
qHGW1-2 27,752 2,960 27752.t000001:
27752.m000045		 AT3G07870.1 F-BOX 92蛋白
F-BOX protein 92
qHGW7-3, qSL7 29,848 849,320 29848.t000145:
29848.m004589		 AT1G80490.2 与在胚胎发生过程中介导生长素依赖的转录抑制密切相关
It is closely related to Topless (TPL), which mediates auxin-dependent transcriptional repression during embryogenesis
qHGW9 28,470 118,469 28470.t000014:
28470.m000435		 AT5G04010 F-box家族蛋白
F-box family protein
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