栽培种花生遗传图谱的构建及主茎高和总分枝数QTL分析

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成良强, 唐梅, 任小平, 黄莉, 陈伟刚, 李振动, 周小静, 陈玉宁, 廖伯寿, 姜慧芳^*
中国农业科学院油料作物研究所 / 农业部油料作物生物学与遗传育种重点实验室, 湖北武汉430062
^* 通讯作者(Corresponding author): 姜慧芳, E-mail:peanut@oilcrops.com, Tel: 027-86711550 第一作者联系方式: E-mail: chengliangmei1984@126.com, Tel: 13971402933
收稿日期:2014-10-27 接受日期:2015-03-19网络出版日期:2015-04-07基金:本研究由国家重点基础研究发展计划(973计划)项目(2011CB109300), 国家自然科学基金项目(31271764, 31371662), 农业部农作物种质资源保护项目(NB2010-2130135-28B), 国家现代农业产业技术体系建设专项(CARS-14-种质资源评价)和山东省农业良种工程(鲁科字[2013]207号)项目资助

摘要栽培种花生是异源四倍体, 基因组大, 构建花生的分子遗传连锁图谱并对相关性状进行QTL定位研究的工作缓慢。本研究以遗传差异大的亲本组配杂交组合富川大花生×ICG6375构建F₂作图群体, 采用公开发表的2653对SSR引物, 构建了一张含有234个SSR标记、分布于20个连锁群的栽培种花生遗传图谱。该图谱覆盖基因组的长度为1683.43 cM, 各个连锁群长度在36.11~131.48 cM之间, 每个连锁群的标记数在6~15个之间, 标记间的平均距离为7.19 cM。结合F₃在湖北武汉和阳逻环境下的主茎高和总分枝数鉴定结果, 应用WinQTLCart 2.5软件采用复合区间作图法进行了QTL定位和遗传效应分析。共检测到17个与主茎高和总分枝数相关的QTL位点, 贡献率在0.10%~10.22%之间, 分布于8个连锁群上。综合分析武汉和阳逻环境的鉴定结果, 获得重复一致的与主茎高相关的6个QTL, 其中 qMHA061.1和 qMHA062.1位于连锁群LG06上TC1A2~AHGS0153标记区间, 贡献率为5.49%~8.95%; qMHA061.2和 qMHA062.2位于LG06上AHGS1375~PM377标记区间, 贡献率为2.93%~5.83%; qMHA092.2和 qMHA091.1位于连锁群LG09上GM2839~EM87标记区间, 贡献率为0.53%~9.43%。

关键词:栽培种花生; 遗传图谱; 主茎高; 总分枝数; QTL
Construction of Genetic Map and QTL Analysis for Mainstem Height and Total Branch Number in Peanut ( Arachis hypogaeaL.)
CHENG Liang-Qiang, TANG Mei, REN Xiao-Ping, HUANG Li, CHEN Wei-Gang, LI Zhen-Dong, ZHOU Xiao-Jing, CHEN Yu-Ning, LIAO Bo-Shou, JIANG Hui-Fang^*
Oil Crops research institute of Chinese Academy of Agricultural Sciences / Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China

AbstractPeanut is an allotetraploid crop with a large genome. The construction of genetic linkage map and QTL mapping of related traits has little progress for peanut. In the present study, a genetic map consisting of 20 linkage groups was constructed with 234 SSR markers based on 2653 published SSR markers by using the F₂population derived from the cross between Fuchuan Dahuasheng and ICG6375. The genetic map covers 1683.43 cM, and the length of each linkage group varies from 36.11 to 131.48 cM, the number of markers in each linkage group varies from 6 to 15, with an average distance of 7.19 cM. Combining with the data of main stem height and number of total branches of F₃ population in the environments of Wuhan and Yangluo, we performed QTL mapping and genetic effects analysis of QTLs by software WinQTLCart 2.5 using CIM (Composite Interval Mapping) method. As a result, 17 QTLs related to main stem height and number of total branches on eight linkage groups were detected with contribution percentage of 0.10%-10.22%. Comparing the QTLs detected in the environments of Wuhan and Yangluo, qMHA061.1 and qMHA062.1were in the same linkage region of markers TC1A2-AHGS0153 of linkage group LG06 with contribution percentage of 5.49%-8.95%, qMHA061.2 and qMHA062.2were between the markers AHGS1375 and PM377 on linkage group LG06 with contribution ratio of 2.93%-5.83%, qMHA092.2 and qMHA091.1 were in the same linkage region of the markers GM2839-EM87 in linkage group LG09 with contribution percentage of 0.53%-9.43%. The QTLs repeatedly detected are important for molecular breeding of peanut.

Keyword:Cultivated peanut; Genetic mapping; Mainstem height; Number of total branches; QTL
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引言分子遗传图谱广泛应用于基因定位、图位克隆以及分子标记辅助育种。栽培种花生(Arachis hypogaea L.)为异源四倍体(2n=40), 因富含脂肪、蛋白质、白藜芦醇等营养保健成分而深受人们的喜爱, 是我国第二大油料作物^{[1, 2]}。在早期的研究中, 由于栽培种花生的DNA多态性相对较为贫乏, 而野生花生的多态性丰富, 因此, 早期的花生遗传图谱的构建多以野生花生为材料^{[3, 4, 5, 6]}。随着SSR标记的大量开发, 近十多年来的研究结果显示, 栽培种花生中也存在较为丰富的遗传多态性。栽培种花生的遗传图谱的构建不断完善, 重要性状QTL的研究报道不断增多。Varshney等^[7]以栽培种花生的RIL群体为材料, 构建了1个包含135个SSR标记的连锁图, 定位了4个与抗干旱相关的QTL。Ravi等^[8]在Varshney构建遗传连锁图谱的基础上增加了56个标记, 构建了包含191个标记的图谱, 定位了13个与干旱抗性成分相关的QTL。Khedikar等^[9]利用栽培种花生的RIL群体构建了一张含有56个SSR标记涉及14个连锁群的遗传图谱, 定位到与抗锈病相关的11个分子标记。Shirasawa等^[10]构建了一张含有1114个位点的栽培种花生遗传图谱, 获得了与开花期、分枝角度、主茎高、荚果长、荚果厚和荚果宽相关的QTL共9个。Wang等^[11]利用栽培种花生的F₂群体构建了一张包含318个标记的遗传图谱, 定位到15个与番茄斑萎病毒(TSWV)相关的QTL, 37个与叶斑病相关的QTL。张新友等^[12]运用栽培种RIL群体和F₂群体定位了与产量和品质性状相关的QTL 62个。综合分析栽培种花生遗传图谱和QTL的研究结果发现, 花生遗传图谱的构建还很不完善, 缺乏高密度的遗传图谱。花生的主茎高和总分枝数是重要的农艺性状, 很多研究结果都表明, 主茎高和总分枝数与产量性状之间存在显著的相关性^{[13, 14]}, 而且主茎高还与植株的抗倒伏性相关。本文以花生的主茎高和总分枝数为调查性状, 采用2个环境下的数据, 拟构建一张遗传图谱, 这对花生的分子设计育种具有重要意义。
1 材料与方法1.1 试验材料根据核心种质的遗传多样性鉴定结果, 选择遗传差异较大的地方龙生型品种富川大花生为母本、从ICRISAT引进的珍珠豆型材料ICG 6375为父本配制杂交组合, 构建218个F₂单株和218个F₃家系的检测群体。
1.2 主茎高和总分枝考察2012年将F₂材料种植于湖北武汉中国农业科学院油料作物研究所试验农场, 单株收获。2013年将上年收获的每个单株材料的种子分成两等份, 分别在武汉中国农业科学院油料作物研究所试验农场和武汉阳逻基地种植成F₃株系。单粒播种, 每行12株, 行长2.0 m, 种植密度为0.4 m× 0.2 m, 常规田间管理。收获时去掉每个株行的边株, 收获中间10株, 按《花生种质资源描述规范和数据标准》^[15]考察主茎高和总分枝数。
1.3 DNA提取及PCR扩增选取幼嫩叶片, 采用改良CTAB法提取DNA, 用1%的琼脂糖凝胶电泳检测DNA浓度与纯度。所用引物序列来源于参考文献^{[16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]}。PCR体系为10 μ L, 含10 mmol L^-1Tris-HCl (pH 8.3)、50 mmol L^-1KCl、300~400 μ mol L^-1 dNTPs、10~40 pmol L^-1引物对、10~20 ng模板DNA。PCR程序为Touchdown, 扩增条件为94℃预变性3 min; 93℃变性30 s, 65℃退火30 s (每个循环-1℃), 72℃延伸1 min, 共10个循环; 93℃变性30 s, 55℃退火30 s, 72℃延伸1 min, 共20个循环; 72℃延伸10 min。PCR产物经6%变性聚丙烯酰胺凝胶电泳检测, 硝酸银染色, 显影, 扫描保存。
1.4 分子标记数据统计统计每份材料扩增的条带, 与母本相同的带型记为“ 1” , 与父本相同的带型记为“ 2” , 同时具有亲本带型的记为“ 3” , 缺失或者不清的带型记为“ 0” 。
1.5 遗传图谱构建及QTL定位运用JoinMap 3.0构建遗传图谱, 首先采用New Project构建新的工作文件夹, 对options内的参数进行设置, 设置LOD≥ 3, 步长设置为0.05; 选择右边的LOD grouping (tree)等选项; 选择population内的create groups for mapping, 即得相应连锁群。连锁分群时应用WinQTLCart2.5复合区间作图法进行QTL定位, 以LOD值≥ 2.5作为检测标准。QTL的命名以性状加所在连锁群加年份命令, 若同一连锁群上出现2个或以上QTL时, 则QTL后面加“ .” 表示, 比如qMHA061.2表示位于LG06连锁群在第1个环境下即武汉环境下检测到的第2个与主茎高相关的QTL。

2 结果与分析2.1 SSR多态性利用已经公开发表的图谱上公布的SSR和EST-SSR引物^{[19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]}共2653对在双亲(富川大花生和ICG6375)中进行筛选, 获得多态性引物275对(表1), 占8.52%。将获得的多态性引物在F₂代群体的218个单株中检测, 共检测到281个位点, 多态率为8.71%。其中AHGS1314、AHGS1470、AHGS1672、AHGS2429、TC6E1和GNB533等6对引物均扩增出了2个位点。
通过统计F₂代群体各单株的带型, 在检测到的281个位点中, 符合孟德尔分离比例的标记共137个, 占48.76%。
2.2 遗传图谱构建根据F₂代群体中检测得到的281个多态性标记, 运用JoinMap 3.0软件进行遗传连锁分析, 获得包含20个连锁群的连锁图(图1), 各连锁群的信息列于表2。在281个多态性标记中, 有234个标记进入连锁群, 47个标记未进入连锁群。构建的图谱总长度为1683.43 cM, 连锁群长度在36.11~131.48 cM之间, 平均每个连锁群长度为84.17 cM; 每个连锁群的标记数在6~15个之间, 平均为11.7个; 相邻两两标记间的平均距离为7.19 cM, 图谱上偏分离标记共116个, 占49.57%。分析各连锁群的长度, 最长的为LG06, 达131.48 cM; 最短的为LG14, 仅36.11 cM。共有9个连锁群的长度> 84.17 cM, 包括LG01、LG09、LG10等, 其余11个连锁群的长度< 84.17 cM。比较分析各连锁群上的标记数, 发现除LG08和LG14这2个连锁群较少外(分别为6个和7个), 其余18个连锁群相对较多, 在9~15个之间。
表2结果还表明, 图谱上的相邻两两标记间的距离不同。相邻两两标记之间的距离≤ 10 cM的有162个, 占69.23%。相邻标记之间距离最小为1.61 cM, 位于LG06连锁群上的GM623与AHGS0153之间; 距离最大为 32.7 cM, 位于同一连锁群(LG06)上的AHGS1512与pPGPseq15D3之间。图谱上偏分离标记分布也不均匀。LG15连锁群上偏分离标记最多, 11个标记发生了偏分离, 占连锁群上标记数目的84.62%。LG04和LG18连锁群上的偏分离标记最少, 均只有2个标记发生了偏分离, 分别占22.22%和20%。
表1
Table 1
表1(Table 1)

表1 引物多态性比例 Table 1 Percentage of polymorphic primers tested

标记类型 Marker type	引物对数 Primer	多态性引物 Polymorphic primers	多态性位点 Polymorphic locus	多态率 Polymorphism rate (%)
SSR	2501	263	277	11.07
EST-SSR	726	12	4	0.55
总计 Total	3227	275	281	8.71

表1 引物多态性比例 Table 1 Percentage of polymorphic primers tested

2.3 表型性状的变异通过对亲本和218个F₃家系的主茎高和总分枝数在武汉和阳逻环境下的鉴定, 获得的结果列于表3。从表3看出, 2个亲本在2种环境下的差异为20 cm左右, 总分枝数相差12条左右。武汉环境下F₃的平均主茎高56.27 cm, 变异范围31.50~87.50 cm; 总分枝数17.66条, 变异范围4.00~61.00条; 主茎高和总分枝数的最高值与最低值间的差异均超出了双亲之间的差异。阳逻环境下F₃的平均主茎高54.30 cm, 变异范围31.00~86.00 cm; 总分枝数18.04条, 变异范围4.30~55.40条; 阳逻环境下的主茎高和总分枝数的最高值与最低值间的差异也均超出了双亲之间的差异。统计分析不同主茎高范围的家系数和不同分枝数范围的家系数, 获得的分布图列于图2。从图2看出, 两种环境下的主茎高分布基本一致, 符合正态分布; 总分枝数的分布也基本一致, 呈偏正态分布。

表2
Table 2
表2(Table 2)

表2 本研究开发的连锁群信息 Table 2 Information of the linkage groups developed in the present study

连锁群 Linkage group	长度 Length (cM)	标记数目 No. of markers	标记间平均距离 Average distance (cM)	偏分离标记 Disorted primers
LG01	92.85	15	6.63	9
LG02	74.87	10	8.32	8
LG03	71.72	13	5.98	6
LG04	74.44	9	9.31	2
LG05	80.21	14	6.17	6
LG06	131.48	13	10.96	7
LG07	70.32	13	5.86	10
LG08	71.75	6	14.35	4
LG09	100.16	12	9.11	4
LG10	113.42	14	8.72	4
LG11	78.25	12	7.11	5
LG12	94.06	12	8.55	4
LG13	89.73	13	7.48	6
LG14	36.11	7	6.02	3
LG15	104.90	13	8.74	11
LG16	62.50	12	5.68	7
LG17	74.98	9	9.37	4
LG18	69.91	10	7.77	2
LG19	85.29	12	7.75	4
LG20	106.50	15	7.61	10
总计	1683.43	234	7.19	116

表2 本研究开发的连锁群信息 Table 2 Information of the linkage groups developed in the present study

图1
Fig. 1

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	图1 花生遗传连锁图谱武汉环境下主茎高QTL; 武汉环境下总分枝数QTL; 阳逻环境下主茎高QTL; 阳逻环境下总分枝数QTL。Fig. 1 Peanut genetic linkage mapQTLs related to mainstem Height in Wuhan; QTLs related to number of total branches in Wuhan; QTLs related to main stem height in Yangluo; QTLs related to number of total branches in Yangluo．

表3亲本以及后代群体性状变异
Table 3Variation of parents and populations traits

环境 Env	性状 Trait	ICG 6375 (父本)	富川大花生 Fuchuan Dahuasheng (母本)	最大值 Max.	最小值 Min.	平均值 Mean	标准差 SD	偏度 Kurt	峰度 Skew	变异系数 CV (%)
武汉 Wuhan	主茎高 Main stem height	65.40	83.60	87.50	31.50	56.27	9.62	0.40	0.46	17.10
武汉 Wuhan	总分枝数 Number of total branches	11.30	23.20	61.00	4.00	17.66	8.65	1.32	3.77	48.98
阳逻 Yangluo	主茎高 Main stem height	62.40	89.30	86.00	31.00	54.30	11.44	0.27	-0.44	21.06
阳逻 Yangluo	总分枝数 Number of total branches	10.80	26.60	55.40	4.30	18.04	9.39	1.06	1.14	52.07

图2武汉和阳逻环境下后代群体主茎高和总分枝数频次分布图
Table 5Common markers of the linkage groups developed from the present study and by Shirasawa (2013)

本研究构建的连锁群 Linkage group from the study	Shirasawa (2013) 整合的连锁群 Linkage group by Shirasawa (2013)	共有标记数 No. of common markers	本研究构建的连锁群 Linkage group from the study	Shirasawa (2013) 整合的连锁群 Linkage group by Shirasawa (2013)	共有标记数 No. of common markers
LG01	A01	7	LG11	B01	10
LG02	A02	5	LG12	B02	8
LG03	A03	8	LG13	B03	9
LG04	A04	6	LG14	B04	6
LG05	A05	7	LG15	B05	11
LG06	A06	9	LG16	B06	10
LG07	A07	10	LG17	B07	4
LG08	A08	4	LG18	B08	8
LG09	A09	8	LG19	B09	10
LG10	A10	9	LG20	B10	13

The authors have declared that no competing interests exist.

作者已声明无竞争性利益关系。The authors have declared that no competing interests exist.

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