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作物学报

作物学报 ›› 2022, Vol. 48 ›› Issue (9): 2180-2195.doi: 10.3724/SP.J.1006.2022.14159

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

基于QTL定位和全基因组关联分析挖掘甘蓝型油菜收获指数相关位点

张超1,2,3(), 杨博1,2, 张立源1,2, 肖忠春1,2, 刘景森1,2, 马晋齐1,2, 卢坤1,2, 李加纳1,2,*()   

  1. 1.西南大学农学与生物科技学院, 重庆 400715
    2.西南大学现代农业科学研究院, 重庆 400715
    3.贵州省农业科学院贵州省油料研究所, 贵州贵阳 550006
  • 收稿日期:2021-09-01 接受日期:2022-01-05 出版日期:2022-09-12 网络出版日期:2022-03-16
  • 通讯作者: 李加纳
  • 作者简介:E-mail: 18083606406@163.com
  • 基金资助:
    国家重点研发计划项目(2018YFD0100500);国家自然科学基金项目(31830067);国家自然科学基金项目(31871653);高等学校学科创新引智基地项目“111”工程项目(B12006);重庆市研究生科研创新项目(CYB20102);重庆市研究生科研创新项目(CYS20124)

Mining harvest index loci based on QTL mapping and genome-wide association study in rapessed (Brassica napus L.)

ZHANG Chao1,2,3(), YANG Bo1,2, ZHANG Li-Yuan1,2, XIAO Zhong-Chun1,2, LIU Jing-Sen1,2, MA Jin-Qi1,2, LU Kun1,2, LI Jia-Na1,2,*()   

  1. 1. College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
    2. Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
    3. Oil Research Institute of Guizhou Province, Guizhou Academy of Agricultural Sciences, Guiyang 550006, Guizhou, China
  • Received:2021-09-01 Accepted:2022-01-05 Published:2022-09-12 Published online:2022-03-16
  • Contact: LI Jia-Na
  • Supported by:
    National Key Research and Development Program of China(2018YFD0100500);National Natural Science Foundation of China(31830067);National Natural Science Foundation of China(31871653);Project of Intellectual Base for Discipline Innovation in Colleges and Universities (111 Project)(B12006);Chongqing Graduate Student Research Innovation Project(CYB20102);Chongqing Graduate Student Research Innovation Project(CYS20124)

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摘要：

收获指数是一个重要的农艺性状, 甘蓝型油菜的收获指数偏低, 有较大的改良空间, 研究油菜收获指数的遗传机理对该性状的改良具有重要的指导意义。本研究利用已构建的高密度遗传图谱对由高、低收获指数亲本衍生而来的包含186个株系的重组自交系进行收获指数的数量性状位点(quantitative trait locus, QTL)定位, 2016—2018连续3年环境及最佳线性无偏预测(best linear unbiased prediction, BLUP)值共定位到12个收获指数相关QTL, 分别位于A03、A05、A06、A07、A09、C04和C05_random染色体上, 单个QTL解释的表型变异在1.27%~14.20%之间。同时, 利用588份重测序自然群体对收获指数性状开展了全基因组关联分析(genome-wide association study, GWAS), 2016、2017、2019年及BLUP值共检测到6个显著关联位点, 分别位于A09、C01和C03染色体上, 其中2019年环境检测到的位于A09上的S9_25882060与S9_25961704重叠, 且与2016年环境检测到的位于A09染色体上的S9_24834640位置接近, 此外2016年环境下GWAS检测到的位点2016HI (S9_24834640)位于2017年环境下重组自交系群体定位的q2017HI-9区段内。对比前人研究, 本研究获得的18个位点中有1个位点与收获指数相关位点重叠, 有6个位点与产量相关性状位点接近。结合本课题组已有的转录组测序结果, 在QTL区段及显著关联的SNP位点附近筛选出36个重点候选基因, 这些基因主要涉及光合作用、跨膜运输、储藏物质合成及转录调控等。这些研究结果为甘蓝型油菜收获指数的遗传改良提供了重要的理论依据。

关键词: 甘蓝型油菜, 收获指数, 全基因组关联分析, 候选基因

Abstract:

Harvest index (HI) is an important agronomic trait, and the HI of rapeseed (Brassica napus L.) remains much lowerer than that of other major crops, indicating there is large scope for improvement of this trait. It is important to explore the genetic mechanism of rapeseed harvest index for its genetic improvement. In this study, QTLs for HI using the 186 recombinant inbred lines (RIL) in the three environments (2016, 2017, and 2018) and best linear unbiased prediction (BLUP) were detected based on the high-density genetic linkage map. A total of 12 HI QTLs located on chromosomes A03, A05, A06, A07, A09, C04, and C05_random were detected, with the explained phenotypic variation of individual QTL range from 1.27% to 14.20%. GWAS for HI was performed using 588 resequencing natural populations established by our previous study. A total of 6 SNPs associated with HI were detected in three years (2016, 2017, and 2019) and BLUP, which located on chromosomes A09, C01, and C03. The S9_25882060 on chromosome A09 detected by the environment in 2019 overlapped with S9_25961704, and was close to S9_24834640 on chromosome A09 detected by the environment in 2016. In addition, 2016HI (S9_24834640) detected in 2016 was located in the interval region of q2017HI-9. Among these 18 loci, one locus was overlapped with reported HI-related QTLs, and six loci were contiguous to reported yield-related QTLs. Combining the results of transcriptome sequencing data of our laboratory, 36 primary candidate genes were selected and these genes involved in the photosynthesis, transmembrane transport, storage components synthesis, transcriptional regulation and so on. These results provide important theoretical basis for genetic improvement of HI in rapeseed.

Key words: Brassica napus, harvest index, GWAS, candidate genes

表1

重组自交系和自然群体甘蓝型油菜收获指数的表型变异"

材料
Material		 环境
Environment		 平均值±标准偏差
Mean±SD		 范围
Range (%)		 变异系数
CV (%)
父本中油821 Male parent Zhongyou 821 2016 17.68±0.95
2017 18.17±4.50
2018 19.68±0.68
母本GH06 Female parent GH06 2016 15.83±0.40
2017 13.06±1.04
2018 16.07±0.42
重组自交系 RIL 2016 20.57±3.29 11.87-32.83 16.01
2017 19.68±4.35 9.33-33.66 22.09
2018 18.50±2.81 9.05-24.02 15.17
BLUP 19.53±1.10 16.03-23.32 5.62
自然群体 NP 2016 17.99±4.35 6.44-29.08 24.18
2017 17.25±4.65 3.55-28.74 26.97
2019 23.14±4.94 5.64-32.73 21.35
BLUP 18.91±3.13 7.80-25.94 16.55

表2

重组自交系和自然群体不同环境条件下收获指数的相关系数"

重组自交系 RIL 自然群体 NP
2016HI 2017HI 2018HI BLUP 2016HI 2017HI 2019HI BLUP
2016HI 1.000 2016HI 1.000
2017HI 0.354** 1.000 2017HI 0.571** 1.000
2018HI 0.269* 0.438** 1.000 2019HI 0.542** 0.594** 1.000
BLUP 0.698** 0.866** 0.733** 1.000 BLUP 0.798** 0.782** 0.800** 1.000

图1

重组自交系和自然群体收获指数频次分布图 RIL: 重组自交系; NP: 自然群体; HI: 收获指数; BLUP: 最佳线性无偏预测。"

表3

甘蓝型油菜收获指数QTL定位结果"

位点
QTL		 染色体
Chr.		 加性效应
Additive effect		 LOD阈值
LOD score		 贡献率
R2 (%)		 标记区间
SNP interval		 物理区间
Physical position (bp)
q2016HI-6 A06 -0.9225 2.5258 7.74 SNP13605-SNP14257 2056287-2944745
q2016HI-7 A07 -1.1539 3.5976 11.18 SNP15424-SNP15485 14920316-15237451
q2016HI-14 C04 3.1475 3.5999 11.53 SNP27560-SNP27571 6005799-6099590
q2017HI-2 A07 -1.1705 2.9408 7.08 SNP3321-SNP3325 12808959-12813162
q2017HI-9 A09 -1.0928 2.7174 5.89 SNP20565-SNP20632 24170241-24935073
q2018HI-5-1 A05 -1.5749 6.0438 14.20 SNP12592-SNP12692 7315852-7543669
q2018HI-5-2 A05 -1.6657 5.2083 11.77 SNP12692-SNP12548 6778798-7543669
q2018HI-15-1 C05_random 0.7312 2.7726 1.27 SNP46328-SNP46308 1679049-1734366
q2018HI-15-2 C05_random 0.7312 2.7726 6.62 SNP46315-SNP46336 1731384-1749200
qBLUPHI-3 A03 -0.4181 3.1453 4.71 SNP5280-SNP5570 10372839-10458202
qBLUPHI-7-1 A07 0.4047 2.7985 5.49 SNP16354-SNP16358 21782147-21797231
qBLUPHI-7-2 A07 0.4000 2.7037 5.31 SNP16342-SNP16345 21687449-21719775

图2

收获指数QTL在连锁群上的位置"

图3

收获指数在各模型下的QQ-plot图及最佳模型下的Manhattan图 HI: 收获指数; BLUP: 最佳线性无偏预测。"

表4

收获指数显著关联位点"

位点
Locus		 染色体
Chr.		 关联标记
Associate marker		 物理位置
Physical position		 贡献率
R2 (%)		 阈值
-log10 (P)		 最佳模型
Best model
2016HI A09 S9_24834640 24,834,640 11.26 5.60 K+Q
2017HI-1 C01 S11_17423943 17,423,943 5.84 5.92 K+Q
2017HI-2 C03 S13_10434536 10,434,536 6.55 5.72 K+Q
2019HI-1 A09 S9_25882060 25,882,060 6.20 5.87 K+PCA
2019HI-2 A09 S9_25961704 25,961,704 5.79 5.69 K+PCA
BLUP_HI C01 S11_28093591 28,093,591 6.36 5.76 K+Q

表5

收获指数候选基因鉴定"

位点
Locus		 物理位置
Physical position		 基因
Genes		 拟南芥同源基因
Homologs in A. thaliana		 功能注释
Functional annotation
q2016HI-6 chrA06: 2056287-2944745 BnaA06g04140D AT1G47960 细胞壁/液泡果糖转化酶的抑制剂,在拟南芥中调节脱落酸响应和耐盐性,在碳水化合物新陈代谢、胁迫响应和糖信号中具有重要作用。
Cell wall/vacuolar inhibitor of fructosidase 1 regulates ABA response and salt tolerance in Arabidopsis, plays important roles in carbohydrate metabolism, stress responses, and sugar signaling.
BnaA06g04150D AT4G29120 6磷酸葡糖糖酸脱氢酶蛋白家族,具有辅酶结合域、氧化还原酶活性、具有磷酸葡糖糖酸脱氢、结合、还原活性。
6-phosphogluconate dehydrogenase family protein possesses coenzyme binding, oxidoreductase activity, phosphogluconate dehydrogenase (decarboxylating) activity, binding, and catalytic activity.
BnaA06g04380D AT1G07890 细胞质APX1,在植物干旱和高温胁迫的适应中具有重要作用。
Cytosolic APX1 plays a key role in the acclimation of plants to a combination of drought and heat stress.
BnaA06g04820D AT1G08380 编码光系统I的O亚基。
Encodes subunit O of photosystem I.
BnaA06g05000D AT1G08630 苏氨酸醛羧酶,涉及降解苏氨酸生成甘氨酸。主要在种子和幼苗中表达。
Threonine aldolase involved in threonine degradation to glycine is primarily expressed in seeds and seedlings.
q2016HI-7 chrA07: 14920316-15237451 BnaA07g18730D AT3G60530 锌指结构转录因子中GATA家族。
GATA factor family of zinc finger transcription factors.
BnaA07g19140D AT3G62100 Aux/IAA蛋白家族,涉及生长素信号途径。促进体细胞胚胎化形成。
Aux/IAA family of proteins implicated in auxin signaling promotes somatic embryogenesis.
BnaA07g19330D AT3G62420 bZIP转录因子53,包含该蛋白的异源二聚体可显著增加种子成熟基因的转录。
The bZIP transcription factor 53 contains Heterodimers containing bZIP53 which participates in enhanceosome formation to produce a dramatic increase in seed maturation gene transcription.
q2016HI-14 chrC04:6005799-6099590 BnaC04g08090D AT2G37170 PIP2质膜镶嵌蛋白亚家族的一个成员。位于质膜上,在爪蟾卵细胞中具有水分转运活性。在维管束中特异表达且蛋白水平在叶片发育过程中显著增加。
A member of the plasma membrane intrinsic protein subfamily PIP2 localized to the plasma membrane exhibites water transport activity in Xenopus oocyte and expresses specifically in the vascular bundles and protein level increases slightly during leaf development.
BnaC04g08100D AT2G37170
q2018HI-5-2 chrA05: 6778798-7543669 BnaA05g11950D AT2G30490 突变该基因影响类苯丙烷的代谢,影响生长和发育。
Mutations in this gene impact phenylpropanoid metabolism, growth, and development.
BnaA05g12160D AT2G30250 WRKY转录因子。涉及响应各种非生物胁迫,特别是盐胁迫。
WRKY transcription Factor which involved in response to various abiotic stresses especially salt stress.
BnaA05g12180D AT2G30200 胚胎缺陷蛋白基因3147,细胞分裂必不可少并且超量表达该基因可增加储藏油脂含量。
Embryo defective 3147 is essential for cell division and its overexpression can increase the storage oil content.
BnaA05g12360D AT2G29980 内质网酶,负责将磷脂合成18:3脂肪酸。
Endoplasmic reticulum enzyme is responsible for the synthesis of 18:3 fatty acids from phospholipids.
BnaA05g12390D AT2G29650 编码位于类囊体膜上的无机磷酸盐转运蛋白PHT4;1。拟南芥中AtPHT4;1通过影响磷酸盐活性影响ATP合成和植物生长。
Encodes an inorganic phosphate transporter (PHT4;1) that is localized to the thylakoid membrane. AtPHT4;1 influences phosphate availability for ATP synthesis and plant growth.
BnaA05g12530D AT2G29500 编码热激蛋白,可以被非生物胁迫例如强光、活性氧、干旱等诱导。
Heat shock proteins encoded can be induced by abiotic stress such as high light, ROS, and drought.
qBLUPHI-3 chrA03: 10372839-10458202 BnaA03g22030D AT2G28840 通过降解热敏元件ELF3来调控热敏性下胚轴生长。侧根萌动所必须。
Regulates thermoresponsive hypocotyl growth through mediating degradation of the thermosensor ELF3. It is required for lateral root initiation.
qBLUPHI-7-2 chrA07: 21687449-21719775 BnaA07g30760D AT1G73260 丝氨酸蛋白酶(Kunitz型)抑制剂,在拟南芥中涉及调控植物病菌侵染的细胞程序性死亡。
Serine protease (Kunitz trypsin) inhibitor which is involved in modulating programmed cell death in plant-pathogen interactions in Arabidopsis.
2016HI
(q2017HI-9)		 chrA09: 24334640-25334640 (chrA09:24170241-24935073) BnaA09g33290D AT3G52930 果糖二磷酸醛缩酶8,拟南芥中其突变会影响胚发育和淀粉合成。
Fructose-bisphosphate aldolase 8, mutations in this gene, impacts embryo development and starch biosynthesis in Arabidopsis.
BnaA09g33720D AT3G53420 过氧化氢的跨膜转运、响应水分缺失、跨膜转运、水分转运。
Hydrogen peroxide transmembrane transport, response to water deprivation, transmembrane transport, and water transport.
BnaA09g34460D AT3G54620 正调控种子成熟,正调控基因转录、DNA模板化。
Positive regulation of seed maturation, positive regulation of transcription, and DNA-templated.
2017HI-1 chrC01: 16923943-17923943 BnaC01g23350D AT3G51520 编码二酰甘油酰基辅酶A转移酶,具有不同骨架酰基辅酶A偏好性,比AtDGAT1将二酰甘油转化成二酰甘油的效率更高。可以在消耗C16:3的基础上增加C18:2和C18:3多不饱和脂肪酸。
Encodes a functional acyl-CoA:diacylglycerol acyltransferase with different acyl-CoA substrate preferences which has higher DAG to TAG conversion rate than AtDGAT1. It increases both C18:2 and C18:3 polyunsaturated fatty acids at the expense of C16:0.
BnaC01g23800D AT3G50820 编码光系统II的外来亚基,对维持具有催化活性的锰离子簇稳定性至关重要。在类囊体上光系统II中的PsbO2不仅对维持光系统II的功能起作用也对调节光系统I与光系统II的比率起作用。
Encodes a protein which is an extrinsic subunit of photosystem II and which has been proposed to play a central role in stabilization of the catalytic manganese cluster. The presence of PsbO2 isoform in the PSII centers has consequences not only to the function of PSII but also to the PSI/PSII ratio in thylakoids.
2017HI-2 chrC03: 9934536-10934536 BnaC03g19670D AT2G35860 类成束阿拉伯半乳聚糖蛋白16前体,在植物次生细胞壁的合成中具有重要作用并且可能涉及胚胎形成和种子发育。
FASCICLIN-like arabinogalactan protein 16 precursor (FLA16) plays a role in plant secondary cell wall synthesis and possibly involved in embryogenesis and seed development.
BnaC03g20550D AT2G37170 PIP2质膜镶嵌蛋白亚家族的一个成员。位于质膜上,在爪蟾卵细胞中具有水分转运活性。在维管束中特异表达且蛋白水平在叶片发育过程中显著增加。
A member of the plasma membrane intrinsic protein subfamily PIP2 which is localized to the plasma membrane has water transport activity in Xenopus oocyte and increases the expressed specifically in the vascular bundles and protein level increases slightly during leaf development.
2019HI-1 chrA09: 25382060-26382060 BnaA09g34720D AT3G54890 编码与光系统I相关的光收集复合体组件。
Encodes a component of the light harvesting complex associated with photosystem I.
BnaA09g34930D AT3G55360 涉及在超长链脂肪酸延长反应中烯脂酰的还原,为表皮蜡质、储藏油脂和鞘脂类代谢所必须。
Enoyl-CoA reductase is involved in all very long chain fatty acids (VLCFA) elongation reactions that are required for cuticular wax, storage lipid, and sphingolipid metabolism.
BnaA09g35240D AT3G55620 涉及在种子休眠过程中响应脱落酸刺激、调控胚胎发育的终止。
Cellular response is related with abscisic acid stimulus and embryo development ending in seed dormancy.
BnaA09g35380D AT3G55800 编码叶绿体酶景天庚酮糖-1,7-二磷酸酶,涉及卡尔文循环的碳还原。增加其活性的转基因株系比对照多积累了50%的蔗糖和淀粉。
The chloroplast enzyme sedoheptulose-1,7-bisphosphatase (SBPase), which involves in the carbon reduction of the Calvin cycle, increases in SBPase activity in transgenic lines accumulate up to 50% more sucrose and starch than wild-type.
BnaA09g35590D AT3G56130 负调控脂肪酸的合成过程。
Negative regulation of fatty acid biosynthetic process.
BnaA09g36130D AT3G56850 编码一个具有bZIP结构域的脱落酸响应元件结合蛋白。定位于细胞核中,在拟南芥种子成熟的胚中表达并涉及调控AtSUC1的表达。
An ABA-responsive element binding protein encodes with a bZIP domain located in the nucleus can regulate the expressed in the embryo during seed maturation and involved in the regulation of AtSUC1 expression in Arabidopsis.
BnaA09g36160D AT3G56860 涉及脱落酸活化信号途径、细胞死亡、防卫反应、乙烯合成过程、叶片衰老、mRNA的稳定化。
Involves abscisic acid-activated signaling pathway, cell death, defense response, ethylene biosynthetic process, leaf senescence, mRNA stabilization.
BnaA09g36180D AT3G56880 响应渗透胁迫、盐胁迫、水分缺失胁迫。
Response to osmotic stress, salt stress and water deprivation.
2019HI-2 chrA09: 25461704-26461704 BnaA09g36610D AT3G57260 响应冷胁迫、系统获得性抗性。
Response to cold, systemic acquired resistance.
BnaA09g36620D AT3G57280 编码位于叶绿体内囊膜的Tmemb-14蛋白家族的一个成员,涉及脂肪酸和油脂的平衡,可能具有从质体中跨膜转运脂肪酸的功能。
A chloroplast inner envelope localized member of the Tmemb-14 gene family is involved in fatty acid and lipid homeostasis, which has likely functions as a fatty acid transporter that exports fatty acids from the plastid.
BLUP_HI chrC01: 27593591-28593591 BnaC01g29930D AT1G61800 葡萄糖-6-磷酸转运,磷酸烯醇式丙酮酸转运,磷酸甘油酸酯跨膜转运,光合作用适应,跨膜运输,磷酸丙糖跨膜转运。
Glucose-6-phosphate transport, phosphoenolpyruvate transport, phosphoglycerate transmembrane transport, photosynthetic acclimation, transmembrane transport, and triose phosphate transmembrane transport.

图4

收获指数主要候选基因的表达热图 CQ: 重庆环境; YN: 云南环境。“24”: 高收获指数材料; “46”: 低收获指数材料。0J: 盛花期中部茎秆; L: 盛花期叶片; 30J: 青荚期中部茎秆; 30CP: 花后30 d侧枝角果皮; 30ZP: 花后30 d主序角果皮; 30CS: 花后30 d侧枝种子; 30ZS: 花后30 d主序种子。FPKM: 每1千个碱基中每百万个比对序列对应目标基因外显子的片段数。"

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