野生大豆保护遗传学基础研究
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摘要
保护遗传学(Conservation Genetics)就是运用遗传学的原理和研究手段,以生物多样性尤其是遗传多样性的研究和保护为研究核心内容的一门新兴学科(Woodruff,1989;1990)。长期以来遗传多样性检测和估算的方法、空间遗传结构与交配系统的关系等基础理论都是保护遗传学研究一直关注的重要问题。本研究以野生大豆这种典型的一年生自交植物为材料,采用不同的研究策略对上述问题开展了三个方面的研究。
(1)利用AFLP、ISSR和SSR三种不同的分子标记分析上海江湾机场的野生大豆自然种群的遗传多样性水平。通过计算机模拟分析,随机抽取不同样本量的抽样群体,判断可以代表种群总体遗传多样性水平的样本大小,对不同分子标记分析结果进行比较,并对各个遗传多样性参数进行评估。
(2)利用17对SSR引物,对上海江湾的两个种群(JW-1和JW-2),北京种群(BJ)和山东垦利种群(KL)共四个种群的1369份样本进行遗传多样性的分析,比较了单个多样性参数与单参数指数系列对这四个种群遗传多样性衡量的差异,并将获得的遗传多样性资料与采样点的地理空间位置结合起来,分析这四个种群的空间遗传结构,包括种群间的遗传分化和用空间自相关分析获得的种群内的遗传斑块结构。
(3)利用5对多态性高的SSR引物对这四个种群中36个家系的1605个子代进行多位点异交率的分析,以获得野生大豆交配系统的基本资料。
基于上述研究,将获得的这四个野生大豆种群的遗传多样性水平、空间遗传结构以及交配系统等情况结合起来进行分析,为制定合理的野生大豆保护策略提供依据。
本研究得到如下结果:
(1)样本量达到30个个体以上才能达到种群总体90%以上的遗传变异,对于小样本种群可以使用无偏估计进行统计校正;
(2)共显性分子标记和显性标记对种群遗传多样性分析的方式不同,分析所得到的各种遗传多样性参数取值范围也不同。在不同分子标记分析的结果之间缺乏可比性;
(3)单个多样性参数不能全面地反映遗传多样性中等位基因频率分布的情况,将用于分析群落物种多样性的单参数指数系列用于研究物种及其种群遗传多样性的衡量和比较具有可行性,可以清晰地反映种群中各个等位基因频率的分布情况;
(4)四个野生大豆种群间存在一定的遗传的分化(F_(st)=0.204);种群内均存在显著空间的遗传斑块(Sp统计值的变异范围在0.036～0.128之间,平均值为0.073)。野生大豆种群内空间遗传斑块的强度和遗传斑块的大小可能受种群的环境异质性以及种群所受干扰程度的影响;
(5)四个野生大豆种群均存在一定的异交,但各个种群的总异交率水平没有显著差异(平均总异交率为14.9%)。进一步剖分交配系统(分为自交、双亲近交和随机异交)发现不同的种群双亲近交率存在较大差别。其中,垦利种群的双亲近交率最高,占总异交率的63%;而JW-1种群的双亲近交率最低,占总异交率的6.7%。说明剖分各种交配方式的比例可以为进一步探讨交配系统的差异提供依据。
(6)结合所研究的四个野生大豆种群的空间遗传结构与其交配系统发现,种群内空间遗传斑块结构对双亲近交所占的比例有较大的影响。遗传斑块越大,斑块结构越强,邻近个体之间的亲缘关系越近,邻近个体发生双亲近交的概率越大;相反亦然。
综合野生大豆遗传多样性水平、遗传结构与交配系统的研究进行分析,在制定野生大豆保护策略特别是原位保护策略时,保持种群生境一定程度的自然扰动可以打破种群内空间遗传结构或是减弱空间遗传结构,这将提高有效异交(effective outcrossing)的频率,增加种群内杂合子的频率,从而维持种群内较高的遗传多样性水平,保持野生大豆的进化潜力。
Conservation genetics is a new subject studying the conservation strategy that makes the nearly extinct or endangered species recover based on the profound knowledge of the genetic background of the species. The estimation of genetic diversity and the relationships between the spatial genetic structure and the mating system are important problems for long term consideration of most conservation geneticists. The wild soybean (Glycine soja), the predominantly self-pollinated species was used as materials to study and explore the problems. At the same time, the knowledge of the genetic background of the wild soybean is the prerequisite for the effective strategic conservation. The following studies had been carried out.
(1) Using three molecular markers (AFLP, ISSR and SSR) to analyze genetic diversity of the wild soybean population in Shanghai Jiangwan district, different molecular markers were compared, and through computer randomly selected subsets with different sample size (5～90 individuals), the proper sample size was evaluated.
(2) Genetic diversity of four wild soybean populations (JW-1, JW-2, BJ, and KL), were studying applying 17 SSR primers. Single genetic diversity index and the One-Parameter Index Families were calculated to exploring the effective methodologies that can be used to compare genetic diversity of different populations. Based on the spatial location of each individual, the spatial genetic structure of the four populations was analyzed, including the genetic differentiation and the fine-scale spatial genetic structure (FSGS).
(3) Basing on 1605 progeny gotten from 36 families, the mating system of the four populations (JW-1, JW-2, BJ, and KL) were estimated by 5 SSR primers. Then according to the knowledge of genetic diversity, spatial genetic structure, and mating system of the four wild soybean populations, the conservation strategy was proposed.
The following items were the main results:
(1) More than 30 individuals were needed to reach 90% of the total genetic diversity of a population. For the small sample size, the unbiased estimation can be used to correct the statistical error.
(2) Codominant molecular markers and the dominant molecular markers had different implication in explaining the genetic diversity and their genetic diversity indices range were different. So it was unreasonable to compare the results gotten by different molecular markers.
(3) The single genetic diversity index can not reflect the allele frequency distributions, but one-parameter index family was a good substitution to evaluate genetic diversity.
(4) There was a certain level of genetic differentiation among different wild soybean populations (F_(st) = 0.204), and there existed a considerable fine-scale spatial genetic structure (FSGS) within each of the four wild soybean populations; the mean Sp value was 0.073, ranging from 0.036 to 0.128, which implying the variation of the FSGS might be caused by the habitat heterogeneity and different levels of disturbances.
(5) There were outcrossing events occurred in all the wild soybean populations and the mean outcrossing rate was 14.9%. Although the total outcrossing rate of these four wild soybean populations didn't have considerable disparity, the detail compositions of the outcrossing rates were divergent ( the KL population had the highest biparent inbreeding 63% and the JW-2 had the lowest only 6.7%).
(6) Combining the results of the spatial genetic structure and the mating system, the conclusion can be drawn that the strength and the size of the FSGS had a deep effects on the mating system. The strong FSGS and large genetic patches may induced high level of biparental inbreeding, which reduced effective outcrossing rate.
In general, a certain degree of disturbances to the natural habitats might be benefited for a plant population to maintain genetic variability and evolutionary potential, which has an important implication in strategic conservation of plant populations.
(1)利用AFLP、ISSR和SSR三种不同的分子标记分析上海江湾机场的野生大豆自然种群的遗传多样性水平。通过计算机模拟分析,随机抽取不同样本量的抽样群体,判断可以代表种群总体遗传多样性水平的样本大小,对不同分子标记分析结果进行比较,并对各个遗传多样性参数进行评估。
(2)利用17对SSR引物,对上海江湾的两个种群(JW-1和JW-2),北京种群(BJ)和山东垦利种群(KL)共四个种群的1369份样本进行遗传多样性的分析,比较了单个多样性参数与单参数指数系列对这四个种群遗传多样性衡量的差异,并将获得的遗传多样性资料与采样点的地理空间位置结合起来,分析这四个种群的空间遗传结构,包括种群间的遗传分化和用空间自相关分析获得的种群内的遗传斑块结构。
(3)利用5对多态性高的SSR引物对这四个种群中36个家系的1605个子代进行多位点异交率的分析,以获得野生大豆交配系统的基本资料。
基于上述研究,将获得的这四个野生大豆种群的遗传多样性水平、空间遗传结构以及交配系统等情况结合起来进行分析,为制定合理的野生大豆保护策略提供依据。
本研究得到如下结果:
(1)样本量达到30个个体以上才能达到种群总体90%以上的遗传变异,对于小样本种群可以使用无偏估计进行统计校正;
(2)共显性分子标记和显性标记对种群遗传多样性分析的方式不同,分析所得到的各种遗传多样性参数取值范围也不同。在不同分子标记分析的结果之间缺乏可比性;
(3)单个多样性参数不能全面地反映遗传多样性中等位基因频率分布的情况,将用于分析群落物种多样性的单参数指数系列用于研究物种及其种群遗传多样性的衡量和比较具有可行性,可以清晰地反映种群中各个等位基因频率的分布情况;
(4)四个野生大豆种群间存在一定的遗传的分化(F_(st)=0.204);种群内均存在显著空间的遗传斑块(Sp统计值的变异范围在0.036～0.128之间,平均值为0.073)。野生大豆种群内空间遗传斑块的强度和遗传斑块的大小可能受种群的环境异质性以及种群所受干扰程度的影响;
(5)四个野生大豆种群均存在一定的异交,但各个种群的总异交率水平没有显著差异(平均总异交率为14.9%)。进一步剖分交配系统(分为自交、双亲近交和随机异交)发现不同的种群双亲近交率存在较大差别。其中,垦利种群的双亲近交率最高,占总异交率的63%;而JW-1种群的双亲近交率最低,占总异交率的6.7%。说明剖分各种交配方式的比例可以为进一步探讨交配系统的差异提供依据。
(6)结合所研究的四个野生大豆种群的空间遗传结构与其交配系统发现,种群内空间遗传斑块结构对双亲近交所占的比例有较大的影响。遗传斑块越大,斑块结构越强,邻近个体之间的亲缘关系越近,邻近个体发生双亲近交的概率越大;相反亦然。
综合野生大豆遗传多样性水平、遗传结构与交配系统的研究进行分析,在制定野生大豆保护策略特别是原位保护策略时,保持种群生境一定程度的自然扰动可以打破种群内空间遗传结构或是减弱空间遗传结构,这将提高有效异交(effective outcrossing)的频率,增加种群内杂合子的频率,从而维持种群内较高的遗传多样性水平,保持野生大豆的进化潜力。
Conservation genetics is a new subject studying the conservation strategy that makes the nearly extinct or endangered species recover based on the profound knowledge of the genetic background of the species. The estimation of genetic diversity and the relationships between the spatial genetic structure and the mating system are important problems for long term consideration of most conservation geneticists. The wild soybean (Glycine soja), the predominantly self-pollinated species was used as materials to study and explore the problems. At the same time, the knowledge of the genetic background of the wild soybean is the prerequisite for the effective strategic conservation. The following studies had been carried out.
(1) Using three molecular markers (AFLP, ISSR and SSR) to analyze genetic diversity of the wild soybean population in Shanghai Jiangwan district, different molecular markers were compared, and through computer randomly selected subsets with different sample size (5～90 individuals), the proper sample size was evaluated.
(2) Genetic diversity of four wild soybean populations (JW-1, JW-2, BJ, and KL), were studying applying 17 SSR primers. Single genetic diversity index and the One-Parameter Index Families were calculated to exploring the effective methodologies that can be used to compare genetic diversity of different populations. Based on the spatial location of each individual, the spatial genetic structure of the four populations was analyzed, including the genetic differentiation and the fine-scale spatial genetic structure (FSGS).
(3) Basing on 1605 progeny gotten from 36 families, the mating system of the four populations (JW-1, JW-2, BJ, and KL) were estimated by 5 SSR primers. Then according to the knowledge of genetic diversity, spatial genetic structure, and mating system of the four wild soybean populations, the conservation strategy was proposed.
The following items were the main results:
(1) More than 30 individuals were needed to reach 90% of the total genetic diversity of a population. For the small sample size, the unbiased estimation can be used to correct the statistical error.
(2) Codominant molecular markers and the dominant molecular markers had different implication in explaining the genetic diversity and their genetic diversity indices range were different. So it was unreasonable to compare the results gotten by different molecular markers.
(3) The single genetic diversity index can not reflect the allele frequency distributions, but one-parameter index family was a good substitution to evaluate genetic diversity.
(4) There was a certain level of genetic differentiation among different wild soybean populations (F_(st) = 0.204), and there existed a considerable fine-scale spatial genetic structure (FSGS) within each of the four wild soybean populations; the mean Sp value was 0.073, ranging from 0.036 to 0.128, which implying the variation of the FSGS might be caused by the habitat heterogeneity and different levels of disturbances.
(5) There were outcrossing events occurred in all the wild soybean populations and the mean outcrossing rate was 14.9%. Although the total outcrossing rate of these four wild soybean populations didn't have considerable disparity, the detail compositions of the outcrossing rates were divergent ( the KL population had the highest biparent inbreeding 63% and the JW-2 had the lowest only 6.7%).
(6) Combining the results of the spatial genetic structure and the mating system, the conclusion can be drawn that the strength and the size of the FSGS had a deep effects on the mating system. The strong FSGS and large genetic patches may induced high level of biparental inbreeding, which reduced effective outcrossing rate.
In general, a certain degree of disturbances to the natural habitats might be benefited for a plant population to maintain genetic variability and evolutionary potential, which has an important implication in strategic conservation of plant populations.
引文
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