全球白菜型油菜遗传多样性分析
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摘要
白菜型油菜是三大类型油菜之一,历史悠久,遗传资源十分丰富,有油用、菜用和饲料用的多种类型,分布广泛。在大量的种植栽培和相对独立的选育后,白菜型油菜的分类异常丰富,包括多种类型及亚种,形态上千差万别,同时具有各种优良特性,如耐贫瘠、耐干旱、抗寒性强,在一些地区具有甘蓝型油菜不可替代的作用。在利用白菜型油菜改良甘蓝型油菜多年以后,在甘蓝型油菜中出现了特定环境下遗传多样性变窄的情况。因此大范围研究白菜型油菜的遗传多样性对于有效保持种质资源多样性和品种选育的长久发展有着重要意义。本实验选取了51对SSR引物对187份来自43个国家的白菜型油菜和5份芸薹属其他作物为对照进行了遗传多样性研究,利用POPGENE和PRIMER 6等软件进行了多样性指标计算和品种聚类分析,并对中国和非中国材料的SSR专属等位基因以及其在基因组的分布情况进行了统计,主要结果如下：
1.187份白菜型油菜表型多样,叶型丰富,其中部分芜菁类材料春化和未春化时表型上差别较大,材料的自交亲和性较差,自交亲和与不亲和的分别有96和91份。
2.农艺性状统计显示非春化材料从播种到开花的周期跨度大,需要40-173天,春化材料跨度相对要小,需要79-153天,而且结束春化到开花过程中,开花期相对集中,最短仅需10天；187份材料中有春性、半冬性和冬性材料各87、73和23份(4份未统计),春性材料春化结束后平均22.3天即开花,而半冬性需要27.8天,冬性材料36.8天。
3.对192份材料SSR扩增产生的数据矩阵进行聚类分析,发现16份材料没有与白菜型油菜聚在一起,而是与甘蓝型油菜或芥菜型油菜等其他芸薹属作物聚在一组；将16份可疑材料与另外16份确认为白菜型油菜的共32份材料,加入18对B基因组引物后重新聚类分析,判断出3份白菜型油菜后,将另外13份非白菜型油菜去除再进行后续分析。
4.174份白菜型油菜共852个等位基因中,来自中国、非中国和对照组材料分别分别有605、704和353个,其中有541个等位基因在中国和非中国两个群体中均有分布；平均每对引物扩增量分别为11.86、13.80和6.92。总的平均扩增量为16.71。
5.中国群体的专属等位基因有64个,富有度为0.74,与芸薹属其他作物共有14个；非中国群体有专属等位基因163个,富有度为1.85,与芸薹属其他作物共有40个；所有材料平均富有度为1.30。
6.基于SSR标记的POPGENE分析结果表明,来自中国和非中国两个群体的总的遗传多样性为0.1118,群体内基因多样性为0.1086,群体间基因多样性为0.0032,基因分化系数为0.0289,基因流为16.7792。两个群体的香浓指数分别为0.1795和0.1959。数据揭示中国和非中国两个种群间变异仅占总种群变异的2.9%,而种群内的变异则为97.1%,品种的种群基因多样性变异主要来源于种群内的变异。
7.基于SSR标记的聚类分析结果为：在遗传距离为0.4360位置将174份材料大致分为4大类。第1和第2大类材料主要来自中国,其中第1大类又可以分为a,b,c三个亚群,分别包括来自中国南方、北方各省区和西南大学新品系；第2大类则主要为中国西北地区材料和邻国的材料；第3大类则主要为印度和欧美国家材料,其中黄籽油菜普遍聚集在一起,包括来自中国的青海大黄油菜；第4大类则主要是遗传距离较远的材料,包括欧美、非洲、中亚和中国少量材料,也包括从奥罗中分离出的A基因组新型材料。不论是用遗传距离还是材料类型或自交亲和等农艺性状,都没有办法将中国的材料和非中国材料明确的区分开。
Brassica rapa L.(n=10, AA genome) is an important oilseed crop, and is also grown as a vegetable and for fodder. Due to its long history of domestication both in Europe and Asia, B. rapa has induced various crop types and subspecies with abundant genetic diversity and elite characteristics, such as adapted to poor land, drought and cold condition, thus B. rapa has played unsubstitutable function. After being made crossed with B. napus for these decades, the diversity among B. napus has been recorded to reduce and become narrower, therefore the analysis of genetic diversity of world-wide B. rapa is meaningful for crop conservation and future breeding development. This study chose 187 accessions of B. rapa from 43 countries and other 5 Brassica species as control, and used 51 pairs of SSR primers to detect the genetic diversity. After obtaining the SSR genotyping data, we analysed the global genetic diversity of B. rapa using the softwares POPGENE and PRIMER 6 and summarized the distribution of the SSR alleles, etc. The experimental results are summaried as follows:
1. The 187 B. rapa accessions have variable phenotypes, especially in leafy shapes. Some turnip accessions diverse heavily between vernalised and non-vernalised materials; most accessions have low self-compatibility, and the number of compatible and incompatible accessions are 96 and 91, respectively.
2. The period from seed sowing to the first flower takes 40-173 days for non-vernalised materials and 79-153 days for vernalised ones; besides, for the vernalised materials, the flowering time is similar and only takes 10 days for the shortest accession. There are 87, 73 and 23(4 unknown) accessions belonging to spring, semi-winter and winter types, and the spring types take about 22.3 days from the end of vernalisation to first flower, while semi-winter and winter type need 27.8 and 36.8 days on average, respectively.
3. Primary cluster analyses are carried out on total 192 accessions, and 16 suspicious accessions are found not to cluster with B. rapa group but with other species such as B. napus or B. juncea. By extra experiment with 18 pairs of B-genome SSR primers for these suspicious accessions and 16 additional B. rapa accessions.3 are identified to be B. rapa after clustering with preliminary A/C genome SSR data and the other 13 are non B. rapa types and excluded from later analysis.
4. There are a total of 852 alleles are detected from 174 B. rapa accessions:The China, Non-China and Control groups have 605,704 and 353 alleles respectively. The average alleles developed by each pair of SSR marker for the three groups are 11.86,13.80 and 6.92, and 16.71 for all accessions.
5. There are 64 private alleles within China group with the richness of 0.74 and 14 are shared with other Brasscia species; and there are 163 private alleles within Non-China groups with the richness of 1.85 and 40 are shared with other Brassica species.
6. The POPGENE calculation based on the matrix data shows that the total gene diversity is 0.1118, the diversity within groups is 0.1086 while the gene diversity among the two groups is 0.0032, and differentiation coefficient and the gene flow is 0.0289 and 16.7792, respectively. The Shannon's Information Indexs is 0.1795 and 0.1959 for China and Non-China groups, respectively. These results revealed that the variations among the two groups only accounted for 2.9% while most variatiori(97.1%) are from within groups.
7. The final cluster based on the SSR matrix data indicates that the 174 accessions can be divided into 4 groups when the GD (genetic distance) is 0.4360. Most accessions in Group 1 and Group 2 are from China, and Group 1 can be divided into another 3 sub-groups (a, b, c), including the accessions most from South China, North China and new materials developed by South West University; Group 2 covers the accessions from Northwest China and China's neighbours; Group3 includes all the Indian accessions and some European or American accessions, most yellow sarson types are clustered together including Qinghai yellow sarson; Group 4 includes most diverse materials coming from Europe, Africa, Middle Asia as well as the new B. rapa derived from Oro. Neither the genetic distance nor phenotypic characters can distinguish China and Non-China types.
1.187份白菜型油菜表型多样,叶型丰富,其中部分芜菁类材料春化和未春化时表型上差别较大,材料的自交亲和性较差,自交亲和与不亲和的分别有96和91份。
2.农艺性状统计显示非春化材料从播种到开花的周期跨度大,需要40-173天,春化材料跨度相对要小,需要79-153天,而且结束春化到开花过程中,开花期相对集中,最短仅需10天；187份材料中有春性、半冬性和冬性材料各87、73和23份(4份未统计),春性材料春化结束后平均22.3天即开花,而半冬性需要27.8天,冬性材料36.8天。
3.对192份材料SSR扩增产生的数据矩阵进行聚类分析,发现16份材料没有与白菜型油菜聚在一起,而是与甘蓝型油菜或芥菜型油菜等其他芸薹属作物聚在一组；将16份可疑材料与另外16份确认为白菜型油菜的共32份材料,加入18对B基因组引物后重新聚类分析,判断出3份白菜型油菜后,将另外13份非白菜型油菜去除再进行后续分析。
4.174份白菜型油菜共852个等位基因中,来自中国、非中国和对照组材料分别分别有605、704和353个,其中有541个等位基因在中国和非中国两个群体中均有分布；平均每对引物扩增量分别为11.86、13.80和6.92。总的平均扩增量为16.71。
5.中国群体的专属等位基因有64个,富有度为0.74,与芸薹属其他作物共有14个；非中国群体有专属等位基因163个,富有度为1.85,与芸薹属其他作物共有40个；所有材料平均富有度为1.30。
6.基于SSR标记的POPGENE分析结果表明,来自中国和非中国两个群体的总的遗传多样性为0.1118,群体内基因多样性为0.1086,群体间基因多样性为0.0032,基因分化系数为0.0289,基因流为16.7792。两个群体的香浓指数分别为0.1795和0.1959。数据揭示中国和非中国两个种群间变异仅占总种群变异的2.9%,而种群内的变异则为97.1%,品种的种群基因多样性变异主要来源于种群内的变异。
7.基于SSR标记的聚类分析结果为：在遗传距离为0.4360位置将174份材料大致分为4大类。第1和第2大类材料主要来自中国,其中第1大类又可以分为a,b,c三个亚群,分别包括来自中国南方、北方各省区和西南大学新品系；第2大类则主要为中国西北地区材料和邻国的材料；第3大类则主要为印度和欧美国家材料,其中黄籽油菜普遍聚集在一起,包括来自中国的青海大黄油菜；第4大类则主要是遗传距离较远的材料,包括欧美、非洲、中亚和中国少量材料,也包括从奥罗中分离出的A基因组新型材料。不论是用遗传距离还是材料类型或自交亲和等农艺性状,都没有办法将中国的材料和非中国材料明确的区分开。
Brassica rapa L.(n=10, AA genome) is an important oilseed crop, and is also grown as a vegetable and for fodder. Due to its long history of domestication both in Europe and Asia, B. rapa has induced various crop types and subspecies with abundant genetic diversity and elite characteristics, such as adapted to poor land, drought and cold condition, thus B. rapa has played unsubstitutable function. After being made crossed with B. napus for these decades, the diversity among B. napus has been recorded to reduce and become narrower, therefore the analysis of genetic diversity of world-wide B. rapa is meaningful for crop conservation and future breeding development. This study chose 187 accessions of B. rapa from 43 countries and other 5 Brassica species as control, and used 51 pairs of SSR primers to detect the genetic diversity. After obtaining the SSR genotyping data, we analysed the global genetic diversity of B. rapa using the softwares POPGENE and PRIMER 6 and summarized the distribution of the SSR alleles, etc. The experimental results are summaried as follows:
1. The 187 B. rapa accessions have variable phenotypes, especially in leafy shapes. Some turnip accessions diverse heavily between vernalised and non-vernalised materials; most accessions have low self-compatibility, and the number of compatible and incompatible accessions are 96 and 91, respectively.
2. The period from seed sowing to the first flower takes 40-173 days for non-vernalised materials and 79-153 days for vernalised ones; besides, for the vernalised materials, the flowering time is similar and only takes 10 days for the shortest accession. There are 87, 73 and 23(4 unknown) accessions belonging to spring, semi-winter and winter types, and the spring types take about 22.3 days from the end of vernalisation to first flower, while semi-winter and winter type need 27.8 and 36.8 days on average, respectively.
3. Primary cluster analyses are carried out on total 192 accessions, and 16 suspicious accessions are found not to cluster with B. rapa group but with other species such as B. napus or B. juncea. By extra experiment with 18 pairs of B-genome SSR primers for these suspicious accessions and 16 additional B. rapa accessions.3 are identified to be B. rapa after clustering with preliminary A/C genome SSR data and the other 13 are non B. rapa types and excluded from later analysis.
4. There are a total of 852 alleles are detected from 174 B. rapa accessions:The China, Non-China and Control groups have 605,704 and 353 alleles respectively. The average alleles developed by each pair of SSR marker for the three groups are 11.86,13.80 and 6.92, and 16.71 for all accessions.
5. There are 64 private alleles within China group with the richness of 0.74 and 14 are shared with other Brasscia species; and there are 163 private alleles within Non-China groups with the richness of 1.85 and 40 are shared with other Brassica species.
6. The POPGENE calculation based on the matrix data shows that the total gene diversity is 0.1118, the diversity within groups is 0.1086 while the gene diversity among the two groups is 0.0032, and differentiation coefficient and the gene flow is 0.0289 and 16.7792, respectively. The Shannon's Information Indexs is 0.1795 and 0.1959 for China and Non-China groups, respectively. These results revealed that the variations among the two groups only accounted for 2.9% while most variatiori(97.1%) are from within groups.
7. The final cluster based on the SSR matrix data indicates that the 174 accessions can be divided into 4 groups when the GD (genetic distance) is 0.4360. Most accessions in Group 1 and Group 2 are from China, and Group 1 can be divided into another 3 sub-groups (a, b, c), including the accessions most from South China, North China and new materials developed by South West University; Group 2 covers the accessions from Northwest China and China's neighbours; Group3 includes all the Indian accessions and some European or American accessions, most yellow sarson types are clustered together including Qinghai yellow sarson; Group 4 includes most diverse materials coming from Europe, Africa, Middle Asia as well as the new B. rapa derived from Oro. Neither the genetic distance nor phenotypic characters can distinguish China and Non-China types.
引文
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