孙倩^,1,2, 邹枚伶², 张辰笈^2,4, 江思容^2,5, Eder Jorge de Oliveira⁶, 张圣奎⁷, 夏志强^,2,3,4,*, 王文泉^,2,3,4,5,*, 李有志^,1,*1广西大学生命科学与技术学院 / 亚热带农业生物资源保护与利用国家重点实验室, 广西南宁 530004
²中国热带农业科学院热带生物技术研究所, 海南海口 571101
³中国热带农业科学院热带生物组学大数据中心, 海南海口 571101
⁴海南大学, 海南海口 570203
⁵南京农业大学, 江苏南京 210095
⁶Embrapa Mandioca e Fruticultura, Cruz das Almas, Bahia 44380-000, Brazil
⁷齐鲁工业大学, 山东济南 250306

Genetic diversity and population structure analysis by SNP and InDel markers of cassava in Brazil

SUN Qian^,1,2, ZOU Mei-Ling², ZHANG Chen-Ji^2,4, JIANG Si-Rong^2,5, Eder Jorge de Oliveira⁶, ZHANG Sheng-Kui⁷, XIA Zhi-Qiang^,2,3,4,*, WANG Wen-Quan^,2,3,4,5,*, LI You-Zhi^,1,*1College of Life Science and Technology / State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning 530004, Guangxi, China
²Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, Hainan, China
³Tropical Bio-omics and Big-Data Center, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, Hainan, China
⁴Hainan University, Haikou 570203, Hainan, China
⁵Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
⁶Embrapa Mandioca e Fruticultura, Cruz das Almas, Bahia 44380-000, Brazil
⁷Qilu University of Technology, Jinan 250306, Shandong, China

通讯作者: * 李有志, E-mail: dyzl@gxu.edu.cn; 王文泉, E-mail: wangwenquan@itbb.org.cn; 夏志强, E-mail: xiazhiqiang@itbb.org.cn

收稿日期:2020-03-13接受日期:2020-08-19网络出版日期:2021-01-12

基金资助:

国家重点研发计划项目.2019YFD1001100 国家自然科学基金-CG联合基金项目.31861143005 滇桂黔石漠化地区特色作物产业发展关键技术集成示范项目.SMH2019-2021 中国热带农业科学院基本科研业务费专项.1630052019022

Received:2020-03-13Accepted:2020-08-19Online:2021-01-12

Fund supported:

National Key Research and Development Project.2019YFD1001100 National Natural Science Foundation of China-CG Joint Fund.31861143005 Key Technology Integration Demonstration Project of Characteristic Crop Industry Development in the Rocky Desertification Area of Yunnan, Guangxi and Guizhou.SMH2019-2021 Special Fund for Basic Scientific Research Operating Expenses of the Chinese Academy of Tropical Agricultural Sciences.1630052019022

作者简介 About authors
E-mail: sunqian9595@163.com











摘要
为了对巴西木薯种质资源进行遗传多样性、亲缘关系和群体遗传结构分析, 本研究利用了7946个SNPs和1997个InDels分子标记, 通过ADMIXTURE软件进行群体结构分析、GCTA软件进行主成分分析。结果显示, 巴西木薯被划分为9个亚群。这与利用PHYLIP进行的聚类分析结果大概一致, 其中亚群1、亚群2、亚群4、亚群6和亚群8能较好地分别聚在一起, 而其他亚群中的样品大致能聚在一起, 且样品间有一定的交叉。巴西木薯种质资源遗传多样性指数(0.274)高于中国、尼日利亚等, 其中巴西木薯亚群5具有相对较高的遗传多样性水平(0.29)。巴西木薯各亚群的群体遗传分化程度较低(群体分化指数在0.03~0.15之间), 但高于中国木薯种质资源的群体分化指数。各木薯材料间的遗传距离变幅为0.084~0.297, 平均遗传距离为0.228。本研究结果可为后续关联分析发掘优良等位基因及引种提供依据。
关键词： 木薯;SNP;InDel;遗传多样性;群体结构

Abstract
As a typical tropical crop, cassava (Manihot esculenta Crantz) has the characteristics of drought resistance, barren resistance, high biomass and so on. In addition to being used for food and forage, it can also be used for production, processing and starch extraction. Due to highly heterozygous cassava genome, breeding is more difficult. Enriching the genetic diversity of cassava germplasm, comprehensively evaluating its genetic background and traits, and discovering superior alleles that control excellent traits are of great significance for cassava breeding in the future. In order to analyze the genetic diversity, genetic relationship and population structure of cassava germplasm in Brazil, 7946 SNPs and 1997 InDels molecular markers were used. Population structure analysis was performed by ADMIXTURE software, and principal component analysis was performed by GCTA software. Brazilian cassava was divided into nine subgroups, and was roughly consistent with the results of cluster analysis using PHYLIP. Among them, subgroup 1, subgroup 2, subgroup 4, subgroup 6, and subgroup 8 could be clustered together respectively, while the samples of other subgroups could be roughly clustered, and there was a certain cross between the samples. The genetic diversity of cassava germplasm in Brazil (0.274) was higher than the genetic diversity level of cassava germplasm in China and Nigeria. Subgroup 5 of Brazil cassava had a relatively high genetic diversity (0.29). The genetic differentiation of subgroups was low (the genetic differentiation vary from 0.03 to 0.15), but higher than domestic cassava germplasm. The genetic distance between cassava accessions varied from 0.084 to 0.297, with the average of 0.228. The results of this study can provide a basis for subsequent association analysis to identify great alleles and introduction.
Keywords：cassava;SNP;InDel;genetic diversity;population structure


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本文引用格式
孙倩, 邹枚伶, 张辰笈, 江思容, Eder Jorge de Oliveira, 张圣奎, 夏志强, 王文泉, 李有志. 基于SNP和InDel标记的巴西木薯遗传多样性与群体遗传结构分析[J]. 作物学报, 2021, 47(1): 42-49. doi:10.3724/SP.J.1006.2021.04067
SUN Qian, ZOU Mei-Ling, ZHANG Chen-Ji, JIANG Si-Rong, Eder Jorge de Oliveira, ZHANG Sheng-Kui, XIA Zhi-Qiang, WANG Wen-Quan, LI You-Zhi. Genetic diversity and population structure analysis by SNP and InDel markers of cassava in Brazil[J]. Acta Agronomica Sinica, 2021, 47(1): 42-49. doi:10.3724/SP.J.1006.2021.04067


木薯(Manihot esculenta Crantz)是大戟科(Euphorbiaceae)木薯属(Manihot P. Mill.)的多年生灌木植物, 具有高生物量、抗贫瘠、抗病虫能力强等特点, 被广泛种植于亚、非、美三洲等多个国家或地区^[1]。木薯起源于亚马逊河流域, 于19世纪20年代传入中国, 最初种植于广东省, 之后逐渐在海南、广西、贵州、云南等地大量种植。它是世界三大薯类作物之一, 同时也是世界上第六大粮食作物, 仅次于小麦、水稻、玉米、马铃薯和大麦^[2]。其用途广泛, 除可食用、饲用外, 还可用于生产加工, 如造纸、纺织、生物燃料等^[3]。木薯块根还可用于提取淀粉, 加工成薯条、面包, 以及生产燃料乙醇等; 茎秆可用来进行木薯繁殖、粉碎还田、做燃料等; 叶片可作蔬菜食用或喂鱼、养蚕等^[4]。

木薯基因组具有高度杂合的特性, 原因是其异花授粉, 且长期进行无性繁殖。由于基因组的高度杂合, 从而增加了木薯遗传变异的多样性, 这些多样性可为木薯育种人员提供更多可选择的良好亲本, 但同时由于木薯的基因组高度杂合、亲缘关系不清晰、遗传改良周期长等特点也增加了育种的工作难度^[5]。目前已有一些利用相关序列扩增多态性(sequence-related amplified polymorphism, SRAP)、简单重复序列(simple sequence repeat, SSR)、扩增片段长度多态性 (amplified fragment length polymorphism, AFLP)、单核苷酸多态性(single nucleotide polymorphisms, SNP)等分子标记进行木薯遗传多样性的研究。Fregene等^[6]利用SSR标记对来源于哥伦比亚、巴西和秘鲁等地的木薯地方品种的种质资源多样性评价发现, 不同国家来源的木薯种质的遗传多样性水平都很高, 其中来自巴西和哥伦比亚材料的基因多样性水平最高。Alex等^[7]利用13对SSR标记对巴西多地的传统甜木薯品种的群体结构和遗传多样性评估结果显示, 该群体的遗传多样性平均值为0.5407, 范围为0.3138 (GA21)~0.6502 (GA140), 表明该群体的遗传变异性宽泛。Carvalho等^[8]采用SSR标记和RAPD标记的研究中发现, 巴西的木薯种质资源的地理来源和遗传聚类具有显著正相关关系。

丰富木薯种质资源的遗传多样性, 并对其遗传背景和性状进行综合评价, 发掘控制优良性状的优异等位基因, 对今后木薯育种具有重大意义。全基因组关联分析(genome-wide association study, GWAS)能够鉴定目的表型性状与遗传标记或基因间的关系, 并检测出控制相关性状的优良等位基因位点^[9]。而进行关联分析需要先评估实验群体的遗传多样性、遗传结构及亲缘关系^[10]。但目前利用SNP和InDel标记对木薯进行遗传多样性、亲缘关系及群体结构分析等的相关研究还鲜为报道。

本研究拟利用SNP和InDel分子标记, 对由巴西Embrapa机构提供的来源于巴西多地的192份木薯种质资源进行遗传多样性和群体结构分析。本研究将为以后木薯育种亲本选配提供材料和理论指导, 也可为下一步通过关联分析发掘控制木薯种质中优良性状的优异等位基因提供理论依据, 从而促进利用分子标记辅助选择技术培育木薯新品种。

1 材料与方法

1.1 试验材料

供试木薯材料共192份, 均为巴西栽培种木薯(表1)。

Table 1
表1
表1192份木薯栽培种
Table 1List of 192 cassava cultivars

编号 No.	名称 Name	编号 No.	名称 Name	编号 No.	名称 Name	编号 No.	名称 Name	编号 No.	名称 Name	编号 No.	名称 Name
001	9624-09	033	BGM0400	065	BGM0783	097	BGM1291	129	BGM1608	161	BGM1942
002	98150-06	034	BGM0405	066	BGM0788	098	BGM1313	130	BGM1615	162	BGM1957
003	BGM0020	035	BGM0408	067	BGM0807	099	BGM1324	131	BGM1622	163	BGM2022
004	BGM0042	036	BGM0425	068	BGM0886	100	BGM1327	132	BGM1626	164	BGM2028
005	BGM0045	037	BGM0428	069	BGM0889	101	BGM1328	133	BGM1640	165	BGM2041
006	BGM0073	038	BGM0436	070	BGM0896	102	BGM1364	134	BGM1662	166	BGM2047
007	BGM0087	039	BGM0443	071	BGM0905	103	BGM1370	135	BGM1667	167	BGM2052
008	BGM0103	040	BGM0451	072	BGM0917	104	BGM1376	136	BGM1668	168	BGM2061
009	BGM0135	041	BGM0452	073	BGM0930	105	BGM1387	137	BGM1672	169	BGM2062
010	BGM0145	042	BGM0467	074	BGM0972	106	BGM1396	138	BGM1679	170	BGM2063
011	BGM0152	043	BGM0495	075	BGM0976	107	BGM1409	139	BGM1682	171	BGM2071
012	BGM0163	044	BGM0501	076	BGM0982	108	BGM1412	140	BGM1684	172	BGM2078
013	BGM0179	045	BGM0507	077	BGM0989	109	BGM1429	141	BGM1690	173	BGM2081
014	BGM0188	046	BGM0523	078	BGM0993	110	BGM1437	142	BGM1697	174	BGM2082
015	BGM0206	047	BGM0540	079	BGM1042	111	BGM1440	143	BGM1698	175	BGM2083
016	BGM0209	048	BGM0542	080	BGM1050	112	BGM1458	144	BGM1704	176	BRS Amansa Burro
017	BGM0211	049	BGM0543	081	BGM1081	113	BGM1485	145	BGM1706	177	BRS Caipira
018	BGM0213	050	BGM0544	082	BGM1106	114	BGM1487	146	BGM1715	178	BRS Dourada
019	BGM0226	051	BGM0550	083	BGM1110	115	BGM1490	147	BGM1722	179	BRS Formosa
020	BGM0250	052	BGM0551	084	BGM1127	116	BGM1495	148	BGM1728	180	BRS Gema Ovo
021	BGM0261	053	BGM0562	085	BGM1153	117	BGM1510	149	BGM1732	181	BRS Jari
022	BGM0264	054	BGM0564	086	BGM1164	118	BGM1524	150	BGM1750	182	BRS Kiriris
023	BGM0269	055	BGM0574	087	BGM1165	119	BGM1535	151	BGM1757	183	BRS Mulatinha
024	BGM0283	056	BGM0600	088	BGM1171	120	BGM1537	152	BGM1760	184	BRS Tapioqueira
025	BGM0288	057	BGM0620	089	BGM1174	121	BGM1539	153	BGM1761	185	BRS Verdinha
026	BGM0331	058	BGM0624	090	BGM1178	122	BGM1549	154	BGM1763	186	Cascuda
027	BGM0336	059	BGM0640	091	BGM1180	123	BGM1552	155	BGM1794	187	Corrente
028	BGM0338	060	BGM0654	092	BGM1193	124	BGM1576	156	BGM1814	188	Eucalipto
029	BGM0352	061	BGM0670	093	BGM1202	125	BGM1581	157	BGM1835	189	Fécula Branca
030	BGM0361	062	BGM0678	094	BGM1226	126	BGM1590	158	BGM1850	190	IAC90
031	BGM0390	063	BGM0726	095	BGM1252	127	BGM1593	159	BGM1883	191	Olho Junto
032	BGM0394	064	BGM0752	096	BGM1281	128	BGM1596	160	BGM1884	192	Valencia

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1.2 木薯基因组DNA提取及建库测序

采用改良的CTAB法^[11]提取木薯叶片的基因组DNA, 经1%的琼脂糖凝胶电泳检测及浓度测定后, 将工作液浓度稀释到100 ng μL^-1, -20℃保存。然后利用AFSM^[12]技术对192份木薯DNA样品使用96孔PCR板分别构建EcoR I-Msp I和EcoR I-Hpa II文库, 单克隆检测达到要求后, 将相应的EcoR I- Msp I和EcoR I-Hpa II文库按1∶1比例混合成1个文库, 总共192个样本, 构建了2个AFSM文库, 并利用Hiseq 2500对构建好的测序文库进行双端150 bp测序。

1.3 SNP和InDels分子标记检测

利用Perl脚本(http://afsmseq.sourceforge.net/)对原始测序数据进行过滤, 同时统计测序得到的总reads数, 再将reads根据AFSM技术设计的Barcodes分配到每个个体中, 并统计每个个体的reads数^[12]。使用Bowtie 2软件^[13]将优化后的测序reads比对到木薯AM560参考基因组^[14], 再使用SAMtools^[15]和VCFtools (http://vcftools.sourceforge.net/)检测SNP和InDels位点。基于木薯AM560参考基因组V6.1, 利用snpEff软件^[16]识别其变异位置(间隔区、非翻译区/UTR、基因上游区或基因下游区)、变异类型(同义突变和错义突变、移码突变和非移码突变), 同时对其进行注释。

1.4 巴西木薯群体结构、遗传多样性及群体分化分析

先利用PHYLIP (http://evolution.genetics.wash-ington.edu/phylip.html)计算样品的遗传距离矩阵, 然后用Notepad++软件将遗传距离矩阵的文件调整成合适的格式, 采用邻接法构建系统进化树结构, 生成tree文件后, 再使用iTOL (https://itol.embl.de/)绘制进化树图。通过GCTA软件^[17]利用检测出的SNP对参试木薯群体材料进行主成分分析(PCA)。再使用R软件计算各个主成分的向量, 绘制PCA散点图。

此外, 使用ADMIXTURE软件^[18]进行群体结构分析, 估算出最佳群体亚群数。先用PLINK软件^[19]调整ADMIXTURE软件的输入文件格式, 并输入文件, 然后将亚群数K值范围设置为1~12, 根据得到的cross-validation error值选择合适的亚群数K值, 利用各个材料占各亚群的遗传成分系数(Q)构成群体遗传结构矩阵。

利用VCFtools软件(https://vcftools.github.io/index.html)计算群体遗传多样性指数(π)和群体分化指数(Fst)^[20]。根据Wright的研究, 当群体分化指数(Fst)等于0或1时, 分别表明亚群间没有分化, 或亚群间完全分化。而当0 < Fst < 0.05、0.05 ≤ FST < 0.15、0.15 ≤ FST < 0.25, 或0.25 ≤ FST < 1时, 则分别表明亚群间具有较弱、中等、比较强或非常强的遗传分化^[21]。

2 结果与分析

2.1 巴西木薯群体基因型分析

通过对192份巴西栽培种木薯基因组DNA进行AFSM建库及测序, 总共得到了155 G数据, 过滤后得到134 G数据, 893,020,018条reads。再利用木薯参考基因组AM560 V6.1, 通过SAMtools和VCFtools软件对192份木薯样品基因组进行扫描, 得到796,006个SNPs和116,821个InDels。

通过哈迪温伯格检测(HWE)>0.001、次等位基因频率(MAF)≥0.05过滤, 并舍去低质量的变异位点后, 仅保留了9443个高质量的变异位点(7946个SNPs和1997个InDels)用于后续分析。其中, 3287个SNPs和InDels位于基因间隔区, 4005个SNPs和InDels位于基因上游区, 471个SNPs和InDels位于基因下游区, 2个SNPs和InDels位于5°端UTR。845个SNPs和InDels属于错义突变, 745个SNPs和InDels属于同义突变, 417个SNPs和InDels属于移码突变, 另有171个SNPs和InDels属于其他类型突变(表2)。

Table 2
表2
表2SNPs和InDels的统计
Table 2Summary of SNPs and InDels

总数 Total	间隔区 Intergenic region	基因上游区 Upstream gene region	基因下游区 Downstream gene region	5'端UTR 5' prime UTR variant	错义突变 Missense variant	同义突变 Synonymous variant	移码突变 Frame shift variant	其他类型 Other types
9443	3287	4005	471	2	845	745	417	171

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2.2 巴西木薯群体结构分析

通过ADMIXTURE软件利用9943个高质量的SNPs和InDels分子标记对192份巴西栽培种木薯进行群体遗传结构分析。将亚群数K值范围设置为1~12, 计算不同K值下的交叉验证错误率(cross-validation error, CV error)。当K从1到2时, CV error值迅速减小; K从2到4时, CV error值又逐渐增加; 当K从4到9时, CV error值逐渐减小并趋于平缓; 当K大于9时, CV error值又出现一定的增幅(图1-a)。说明在K等于9时, CV error值最小, 因此巴西栽培种木薯群体可分为9个亚群(Subgroup 1~Subgroup 9)。

图1

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图1192份木薯品种的群体遗传结构

a: 利用ADMIXTURE软件对192份木薯材料进行群体结构分析, 计算K为1~12时的CV error。b: K = 9时的群体结构, 在该群体结构中, 每个个体用一根带有9种不同颜色的线表示, 根据颜色的占比推断该品种属于哪个亚群, 红、橙、黄、绿、蓝绿、湖蓝、深蓝、紫、紫红色分别代表亚群1~9。c: 利用高质量变异位点对192份巴西木薯进行主成分分析, 每一个点代表一份样品, 橙色、桔色、黄色、草绿、深绿、天蓝、深蓝、紫和紫红色分别代表亚群1~9 (根据ADMIXTURE软件推断的结果)。
Fig. 1Population genetic structure of 192 cassava cultivars

a: ADMIXTURE was used to analyze the population structure of 192 cassava materials, and the cross-validation error was calculated when K was 1-12. b: The population structure at K = 9, in this population structure, each individual is represented by a line with multiple different colors, and the subgroup to which the individual belongs is inferred based on the proportion of the color, the nine color regions arranged from left to right in order represent subgroups 1 to 9, respectively. c: Principal component analysis (PCA) of the group, one point represents an individual, nine colors and their corresponding shapes represent different subgroups.


192份巴西木薯可以被分为9个亚群, 再根据每个个体在这9个亚群的Q值, 将每个个体归类到Q值最大所在的亚群(图1-b)。9个亚群中分别含有3份、22份、27份、6份、20份、25份、24份、12份和53份材料。

主成分分析以所有的高质量SNPs和InDels为基础, 通过R软件分析绘图, 得到如下结果: 该木薯群体的9个亚群在PC1轴上可以看出一定的分布差距, 大部分亚群可以聚类在一起, 该结果说明聚类结果与群体结构的划分具有一致性(图1-c)。

由图2可知, 聚类结果与群体结构的划分相一致, 亚群1、亚群2、亚群4、亚群6和亚群8能较好地分别聚在一起, 而其他亚群样品大致能聚在一起, 且样品间有一定的交叉。巴西木薯各栽培种之间并未聚类到一起, 可能是由于木薯栽培历史比较短, 来源于巴西多地的木薯栽培种还未产生明显的分化。

图2

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图2192份巴西栽培种木薯系统进化树图

淡蓝色、深蓝色、草绿色、深绿色、肉色、橙色、紫红色、红色和紫色分别代表亚群1~9。
Fig. 2Phylogenetic tree of 192 cassava cultivars from Brazil

Light blue, dark blue, grass green, dark green, flesh, orange, fuchsia, red, and purple represent subgroup 1 to 9, respectively.

2.3 巴西栽培种木薯遗传多样性分析

利用9943个高质量的SNPs和InDels, 通过计算遗传多样性指数(π), 评估巴西栽培种木薯群体和各个亚群的遗传多样性。通过vcftools计算发现, 巴西栽培种木薯群体的遗传多样性指数为0.274, 亚群1~9的遗传多样性指数在0.192~0.289之间, 其中亚群1具有最低的遗传多样性指数(0.192), 亚群7、亚群2、亚群6和亚群3具有相对较高的遗传多样性指数, 分别达到0.284、0.281、0.264和0.261, 而亚群5具有9个亚群中最高的遗传多样性指数(0.289) (表3)。说明巴西栽培种木薯群体具有相对较高的遗传多样性水平。

Table 3
表3
表3遗传多样性指数(π)的统计
Table 3Statistics of genetic diversity index (π)

亚群 Subgroup	π
1	0.192
2	0.281
3	0.261
4	0.221
5	0.289
6	0.264
7	0.284
8	0.209
9	0.234
整体Entirety	0.274
平均Average	0.248

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利用群体分化指数(Fst)评估巴西栽培木薯亚群间的差异程度(表4)发现, 除亚群1和亚群4之间有较强遗传分化外, 其他亚群之间均为中等或较弱遗传分化, 亚群间的遗传分化指数在0.031~0.152之间。其中, 亚群8与其他各亚群之间均为中等分化; 而除亚群4与亚群1外, 亚群4和亚群1分别与其他各亚群之间也均为中等分化。表明, 除亚群1与亚群4间遗传分化较强、亲缘关系较远外, 其余各亚群间的为中等或较弱遗传分化程度, 即亚群间的亲缘关系相对均较近。

另外, 本研究对试验所用的巴西栽培木薯的遗传距离分析发现, 这些木薯种质间的遗传距离为0.084~0.297, 平均遗传距离为0.228。其中, BGM 1883与Valencia遗传距离最近(0.084); BGM0640与BRSJari遗传距离最远(0.297)。

Table 4
表4
表4群体分化指数(Fst)的统计
Table 4Statistics of population differentiation index (Fst)

亚群Subgroup	1	2	3	4	5	6	7	8	9
1
2	0.065
3	0.081	0.061
4	0.152	0.073	0.112
5	0.053	0.032	0.069	0.062
6	0.058	0.045	0.033	0.086	0.041
7	0.059	0.038	0.054	0.078	0.031	0.045
8	0.139	0.085	0.076	0.119	0.084	0.056	0.080
9	0.058	0.043	0.046	0.083	0.048	0.034	0.038	0.061

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3 讨论

3.1 木薯群体结构分析

研究表明, 基因型与性状之间会产生假关联, 其原因可能是群体结构分层、等位基因分布不均等^[22]。为了消除造成关联分析不准确的因素, 我们需要先对试验群体进行群体结构分析。本研究利用ADMIXTURE软件对巴西木薯自然群体的群体结构分析表明, 当K=9时, CV error值最小, 由此将192份木薯种质划分为9个亚群, 该结果与聚类分析、主成分分析的结果大概相符, 它们之间相互补充及印证, 说明该木薯群体的遗传结构较为可靠。在这9个亚群中, 群体分化指数在0.03~0.15之间, 且大部分亚群间的群体分化指数均小于0.09, 表明该木薯群体存在一个中等偏弱的遗传分化。前人的研究结果显示, 中国热带农业科学院热带品种资源种质圃收集的158份木薯种质的群体分化指数在0.03~0.07之间^[23]; 在其他地区的栽培木薯中, 群体分化指数在0.01~0.05之间^[14], 表明国内收集的木薯遗传分化程度较低。比较看来, 本研究中的巴西木薯种质的群体分化指数高于国内收集的木薯种质, 可挑选优质巴西木薯品种并引进中国, 从而丰富已有的木薯种质资源。

3.2 木薯遗传多样性分析

本研究对遗传多样性指数(π)进行了计算, 从而评估该木薯群体的遗传多样性。Ramu等^[14]的研究表明, 来源于不同地区(尼日利亚、哥伦比亚、巴西等地)的国外栽培木薯的遗传多样性指数为0.0036, 低于其祖先(M. esculenta ssp. flabellifolia, π = 0.0051); Fregene等^[6]对来源于哥伦比亚、巴西和秘鲁等地的木薯地方品种的种质资源多样性评价发现, 巴西和哥伦比亚的木薯种质具有最高的遗传多样性水平; 在张圣奎对中国热带农业科学院热带品种资源种质圃收集的158份木薯种质的遗传多样性研究中发现, 该群体的遗传多样性指数为1.21×10^-4, 表明该群体的遗传多样性较低^[23], 同时也表明目前国内的木薯种质资源丰富度较为缺乏。本研究发现, 该巴西木薯群体中各亚群的遗传多样性指数在0.19~0.29之间, 平均遗传多样性指数为0.248, 说明巴西木薯群体的遗传多样性较为丰富, 可引进部分优良巴西种质以丰富国内的木薯种质资源。除此之外, 样本之间的亲缘关系也会对关联分析的结果造成一定的影响。本研究对192份木薯种质间的遗传距离进行分析, 从而评估不同材料之间的亲缘关系, 结果发现这些木薯种质的平均遗传距离为0.228。

4 结论

本研究利用9943个高质量的SNPs和InDels对192份巴西Embrapa机构提供的木薯种质进行了和群体遗传结构分析。遗传多样性分析结果显示, 巴西木薯群体的遗传多样性水平较为丰富, 高于中国和哥伦比亚等地区; 群体遗传结构分析结果显示, 该群体被划分为9个亚群, 此结果与主成分分析及聚类分析结果基本一致。另外, 该木薯群体的分化程度较低, 但高于国内的木薯种质资源。遗传距离分析显示, BGM1883与Valencia遗传距离最近, BGM0640与BRSJari遗传距离最远。该研究将为之后关联分析挖掘优良基因及引进优良巴西木薯种质提供依据。

参考文献 View Option 原文顺序
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