利用SRAP标记研究海南野生稻的遗传多样性与遗传分化

利用8对多态性较好的SRAP引物对海南120份普通野生稻、55份疣粒野生稻和26份药用野生稻进行扩增,在检测到的219个位点中,普通野生稻的多态性位点率为74.89％,疣粒野生稻为42.47％,药用野生稻25.11%。香农指数以普通野生稻最高0.3277,疣粒野生稻为0.2044,药用野生稻最低0.1113。UPGMA聚类分析结果显示供试材料与地理来源相一致,相关性强,各居群个体间没有出现任何交叉。根据居群间的遗传分化系数,普通野生稻群体的基因多样性为0.2135,群体内的平均基因多样性大于居群间的基因漂变,说明普通野生稻居群遗传分化不显著,遗传多样性主要来自于居群内,基于群体杂合度和居群遗传多样性指数特点,认为实施保护策略时,优先保护遗传多样性最丰富的WDL和WDA居群。疣粒野生稻居群存在中等程度的遗传分化,建议原生境保护;药用野生稻居群数量较少,建议原生境保护。     

云南疣粒野生稻的居群遗传结构及其在原位保护中的意义

用 1 2种酶系统 1 7个等位酶位点对采自云南思茅地区疣粒野生稻Oryzameyeriana(Zoll.etMerr.exSteud .)Baill.7个居群的 1 6 4个个体进行了遗传多样性的研究 .相对于以前报道过的具有相同生活史特性和繁育系统的种子植物和稻属中的其他种类 ,疣粒野生稻的遗传多样性水平极低 (A =1 .1 ,P =8.0 % ,H_o=0 .0 0 4和H_e=0 .0 1 5 ) ,但居群间的遗传分化较大 .F_ST高达 0 .6 4 9,表明在遗传变异总量中的6 4 .9%存在于居群间 .对这样在较小的地理区域内居群间就呈现出剧烈遗传分化的物种来说 ,大多居群均有保护的价值 .因此 ,进行原位保护时原则上应建立较大的自然保护区 ,涉及较多数目的居群 .同时 ,提出了在云南进行原位保护时应优先考虑的地点 .     

云南元江普通野生稻(Oryza urfipogon Griff)遗传多样性分析及保护策略研究

用SSR方法对云南元江普通野生稻3个自然居群进行30个位点的遗传多样性分析.结果表明,元江普通野生稻具有较高的遗传变异水平(Ap＝2.6,Hs=0.77),且群体遗传分化系数较大,GST为41.08%,即在遗传变异总量中41.08%存在于居群间.本文还通过对云南元江普通野生稻遗传多样性特点的分析,提出了保护策略.     

广西武宣濠江流域普通野生稻居群遗传多样性及保护研究

选用平均分布于水稻基因组的24对SSR引物,对沿河分布最长的广西武宣濠江流域的12个普通野生稻居群343份材料的遗传结构进行研究.结果表明:(1)该地普通野生稻遗传多样性丰富.24个位点共检测到206个等位变异,平均等位变异数A＝8.7083,有效等位变异数Ae＝3.7117;(2)该地普通野生稻居群具有较高的遗传分化和一定频率的基因流.群体遗传分化系数Gst＝0.2659,基因流Nm＝0.6901,表明26.59%的遗传变异存在于居群间;(3)SSR标记使普通野生稻居群中一些稀有等位变异得以显现.206个等位变异中,65个等位变异仅出现在1个或2个居群中,且频率较低,其中12个等位变异只出现在居群B中;(4)通过聚类分析和主坐标分析(PCO),下游居群A和B遗传关系较近,中游居群C比较独特,单独成为一类,中游居群D、E、F和G遗传关系较近,中游居群H、I和J及上游居群K和L遗传关系较近.根据上述分析结果,建议对濠江下游和中游具有代表性的居群(即居群B、D和H)的普通野生稻进行重点保护.     

云南灯盏花遗传变异的RAPD分析

运用RAPD (randomamplifiedpolymorphicDNA)技术对云南灯盏花 (Erigeronbrevis capus) 6个居群进行分析 ,研究其遗传变异及遗传结构 ,用外类群紫菀对比分析其亲缘关系。随机挑选 16个引物在 6个居群中共产生 2 33条DNA片段 ,其中 192条带具有遗传多态性 ,约占 82 4 0 %。多态位点百分比PPB、等位基因数A、有效等位基因数Ae、Nei’s基因多样性指数H和Shannon多样性指数I在物种水平分别为 82 4 0 %、 1 82 4 0、 1 30 0 5、0 1896、 0 30 2 1;居群的平均值分别为 5 4 2 3%、 1 5 40 1、 1 2 6 91、 0 16 0 7、 0 2 4 6 0。灯盏花的遗传多样性较丰富 ,基因分化系数Gst值为 0 346 0 ,有 6 5 4 0 %的变异来自居群内 ,6个居群的遗传一致度较高 ,在 0 90 37～ 0 972 3之间 ,平均为 0 94 10。利用UPGMA对 6居群聚类分析 ,结果表明 :丘北居群 (YB)和文山居群 (YX)亲缘关系最近 ,小哨居群 (Y )和新平居群 (YA)次之 ,丘北居群 (YB)和腾冲居群 (ZA)亲缘关系最远。遗传关系与各居群地理分布区间的距离大致成正相关     

SSR 在琼海和三亚两普通野生稻居群中的遗传变异

通过分析37个SSR座位在琼海与三亚两普通野生稻(Oryza rufipogon)居群中的遗传变异, 结果表明, SSR座位在三亚普通野生稻居群中的变异高于其在琼海普通野生稻居群中的变异。根据遗传相似性和遗传距离公式得到琼海与三亚普通野生稻居群间的遗传相似性为0.6385, 遗传距离为0.4486 cM。Wright的FST检验结果表明, 这37个SSR座位在两居群之间存在着中等程度的遗传分化, FST=0.3909。此分化结果主要是由两居群间弱的基因漂移导致的(Nm=0.3895)。     

广东高州普通野生稻(Oryza rufipogon Griff)的遗传多样性和居群遗传分化研究

利用30对SSR引物对广东高州普通野生稻3个群体进行了遗传多样性分析和居群遗传分化研究.结果表明,30对引物中只有20对表现出多态,多态位点比率P为66.7%;在20个多态位点中共检测出81个等位变异,平均等位变异数(Ap)为4.05 个;3个群体总的遗传多样性(Ht)为0.61,其中,居群内的遗传多样性为居群间的遗传多样性的3倍多,说明总的遗传多样性主要来自居群内;虽然居群间的遗传分化系数(G ST)较低,仅为0.2427,但当遗传相似系数临界值增加时,3个群体在聚类图上相对独立 ,说明3个群体既存在着高度的遗传相似性,又具有一定程度的遗传分化,可以作为3个居群进行原生境保护.     

SSR在琼海和三亚两普通野生稻居群中的遗传变异

通过分析37个SSR座位在琼海与三亚两普通野生稻（Oryza rufipogon）居群中的遗传变异,结果表明,SSR座位在三亚普通野生稻居群中的变异高于其在琼海普通野生稻居群中的变异。根据遗传相似性和遗传距离公式得到琼海与三亚普通野生稻居群间的遗传相似性为0．6385,遗传距离为0．4486cM。Wright的啪验结果表明,这37个SSR座位在两居群之间存在着中等程度的遗传分化,FST=0．3909。此分化结果主要是由两居群间弱的基因漂移导致的（Nm=0．3895）。     

基于SSR分子标记的延胡索遗传多样性研究

采用SSR分子标记分析延胡索的遗传多样性,筛选出多态性高、稳定性好的12对引物,对19个居群360份延胡索样品进行了群体遗传分析。结果表明:(1)12对SSR引物共扩增出多态性位点227个,检测到4~9个等位基因,平均等位基因数目为5.25个,表现出丰富的多态性;延胡索居群具有较高的遗传多样性(Na=5.25,I=1.192 6,H=0.387 9),物种间遗传分化程度高(Fst=0.388 3),基因流较弱(Nm=0.393 8)。(2)UPGMA聚类分析和贝叶斯距离分析结果表明,19个居群明显聚为4大支;Mantle Test结果(r=0.326,P=0.01)表明,地理位置相近的种群亲缘关系更近。研究认为,延胡索的遗传结构是该物种自交为主的繁育系统、克隆生长、地理隔离以及居群间有限的基因流共同作用的结果,故对该物种的保护应以就地保护为主。     

云南南部不同种源地小桐子遗传多样性的ISSR分析

应用ISSR分子标记方法对采自云南的8个居群的小桐子(Jatropha curcas)共158个个体进行遗传多样性分析。8个ISSR引物共扩增到了67个位点,其中61个是多态性位点。分析结果表明:(1)云南小桐子的遗传多样性水平很高。在物种水平上,平均每个位点的多态位点百分率PPB=91.04%,有效等位基因数Ne=1.5244,Nei′s基因多样性指数He=0.3070,Shannon多样性信息指数Ho=0.4618;在居群水平上,PPB=55.04%,Ne=1.3826,He=0.2171,Shannon多样性信息指数Ho=0.3178。(2)居群间的遗传分化低于居群内的遗传分化。基于Nei′s遗传多样性分析得出的居群间遗传多样性分化系数Gst=0.2944。AMOVA分析显示:云南小桐子的遗传变异主要存在于居群内,占总变异的63.50%,居群间的遗传变异占36.50%。(3)居群间的地理距离及遗传一致度并不存在相关性。鉴于以上指标,我们推测云南小桐子可能来自不同的地区。     

居群遗传结构研究中显性标记数据方法初探

为对比显性标记应用于居群遗传结构研究时不同统计参数的适用性,利用RAPD技术对中国5个居群的100个疣粒野生稻个体进行了遗传结构分析。在衡量居群遗传多样性水平时,多态位点比率（PPB）会低估遗传变异的量,其价值不如Shannon多样性指数和Nei基因多样性指数,而采用Nei指数时不必进行Lynch-Milligan矫正。对个体间遗传关系进行分析时,17种遗传相似性指数矩阵两两之间的Mantel检测都表现出极显著的相关性（r＞0.95,t＞t     

中国疣粒野生稻的分布、濒危现状和保护前景

继1978-1982年全国野生稻普查后,又一次对中国疣粒野生稻（Oryza granulata (Nees et Arn.Ex Watt.））主要分布点的居群特征、濒危现状和破坏情况进行了野外生态学研究。由于行政区划的改变,目前疣粒野生稻在中国分布的市（县）达30个。它在群落盖度为90%-210%下生长良好,具有抗旱和适应中度干扰的能力。聚集参数分析表明在群落中居群以集群分布为主。该物种主要通过重力和动物传播种子,居群间的基因流有限,形成了典型的集合种群（metapoulation）结构。生境丧失对疣粒野生稻的生长造成非常严重的后果,巳有12.9%的疣粒野生稻居群灭绝,83.9%的居群处于中度和重度的干扰之下。由于各地区的破坏程度不平衡,目前疣粒野生稻的分布被压缩到海南省的西南部山区和云南省和澜沧江中下游、南汀河流域,面临热区开发的巨大威胁。研究中建立了中国疣粒野生稻的总DNA库,作为易位保护的手段之一和开展保护遗传学研究的基础;并讨论了居群遗传结构与居群分布格局之间的相互关系和保护中需注意的问题。     

Diversity in the Content of Some Nutritional Components in Husked Seeds of Three Wild Rice Species and Rice Varieties in Yunnan Province of China

In addition to rice (Oryza sativa L.) cultivars, there are three wild rice species, namely O.rufipogon Griff, O. officinalis Wall and O. granulata Baill, in Yunnan Province, China. Each species has different subtypes and ecological distributions. Yunnan wild rice species are excellent genetic resources for developing new rice cultivars. The nutritional components of the husked seeds of wild rice have not been investigated thus far. Herein, we report on the contents of total protein, starch, amylose, 17 amino acids, and five macro and five trace mineral elements in husked seeds from three wild rice species and six O. sativa cultivars. The mean (± SD) protein content in the husked rice of O. rufipogon, O. officinalis, and O. granulata was (14.5 ± 0.6)%, (16.3 ± 1. 1)%, and (15.3 ± 0.5)%, respectively. O. officinalis Ⅲ originating from Gengma had the highest protein content (19.3%). In contrast, the average protein content of six O. sativa cultivars was only 9.15%. The total content of 17 amino acids of three wild rice species was 30%-50% higher than that of the six cultivars. Tyrosine, lysine, and valine content in the three wild rice species was 34%-209% higher than that of the cultivars. However, the difference in total starch content among different O. sativa varieties or types of wild rice species was very small. The average amylose content of O. rufipogon, O. officinalis,and O. granulata was 12.0%, 9.7%, and 11.3%, respectively, much lower than that of the indica and japonica varieties (14.37%-17.17%) but much higher than that of the glutinous rice cultivars (3.89%). The sulfur, phosphorus, magnesium, zinc, and ferrite content in the three wild rice species was 30%-158% higher than that of the six cultivars. The considerable difference in some nutritional components among wild rice species and O. sativa cultivars represents a wide biodiversity of Yunnan Oryza species. Based on the results of the present study, it is predicted that some good genetic traits, especially high protein and ideal amylose content, of Yunnan wild rice species may be useful in improving the nutritional value of rice. This is the first report regarding the amino acid, mineral element, protein and amylose content of husked seeds of some Yunnan wild rice species that have important genetic characteristics for rice quality and nutritional value.     

SNP haplotypes of the <Emphasis Type="Italic">BADH1</Emphasis> gene and their association with aroma in rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.)

Betaine aldehyde dehydrogenase (BADH) is a key enzyme involved in the synthesis of glycinebetaine—a powerful osmoprotectant against salt and drought stress in a large number of species. Rice is not known to accumulate glycinebetaine but it has two functional genes coding for the BADH enzyme. A non-functional allele of the BADH2 gene located on chromosome 8 is a major factor associated with rice aroma. However, similar information is not available regarding the BADH1 gene located on chromosome 4 despite the similar biochemical function of the two genes. Here we report on the discovery and validation of SNPs in the BADH1 gene by re-sequencing of diverse rice varieties differing in aroma and salt tolerance. There were 17 SNPs in introns with an average density of one per 171 bp, but only three SNPs in exons at a density of one per 505 bp. Each of the three exonic SNPs led to changes in amino acids with functional significance. Multiplex SNP assays were used for genotyping of 127 diverse rice varieties and landraces. In total 15 SNP haplotypes were identified but only four of these, corresponding to two protein haplotypes, were common, representing more than 85% of the cultivars. Determination of population structure using 54 random SNPs classified the varieties into two groups broadly corresponding to indica and japonica cultivar groups, aromatic varieties clustering with the japonica group. There was no association between salt tolerance and the common BADH1 haplotypes, but aromatic varieties showed specific association with a BADH1 protein haplotype (PH2) having lysine₁₄₄ to asparagine₁₄₄ and lysine₃₄₅ to glutamine₃₄₅ substitutions. Protein modeling and ligand docking studies show that these two substitutions lead to reduction in the substrate binding capacity of the BADH1 enzyme towards gamma-aminobutyraldehyde (GABald), which is a precursor of the major aroma compound 2-acetyl-1-pyrroline (2-AP). This association requires further validation in segregating populations for potential utilization in the rice breeding programs.     

High levels of genetic differentiation of Oryza officinalis Wall. ex Watt. from China

In order to determine the population genetic structure of wild rice (Oryza officinalis Wall. ex Watt.), an endangered tropical and subtropical species, allozyme diversity encoded by 24 loci was analyzed electrophoretically in 145 individuals of eight natural populations from Hainan, Guangxi, and Yunnan provinces, China. A fairly high genetic differentiation (F(ST) = 0.882 and mean I = 0.786) was found among the studied populations. Our results suggest that restricted gene flow may play a significant role in shaping such a population genetic structure. In addition, high genetic differentiation among populations within a geographically limited region may stem from a reduced population size and consequent genetic drift.     

Molecular analysis of the NAC gene family in rice

Genes that encode products containing a NAC domain, such as NO APICAL MERISTEM (NAM) in petunia, CUP-SHAPED COTYLEDON2 (CUC2) and NAP in Arabidopsis thaliana, have crucial functions in plant development. We describe here molecular aspects of the OsNAC genes that encode proteins with NAC domains in rice (Oryza sativa L.). Sequence analysis revealed that the NAC genes in plants can be divided into several subfamilies, such as the NAM, ATAF, and OsNAC3 subfamilies. In rice, OsNAC1 and OsNAC2 are classified in the NAM subfamily, which includes NAM and CUC2, while OsNAC5 and OsNAC6 fall into the ATAF subfamily. In addition to the members of these subfamilies, the rice genome contains the NAC genes OsNAC3, OsNAC4 (both in the OsNAC3 subfamily), OsNAC7, and OsNAC8. These results and Southern analysis indicate that the OsNAC genes constitute a large gene family in the rice genome. Each OsNAC gene is expressed in a specific pattern in different organs, suggesting that this family has diverse and important roles in rice development.     

Effects of natural selection on interpopulation divergence at polymorphic sites in human protein-coding Loci

To develop new strategies for searching for genetic associations with complex human diseases, we analyzed 2784 single-nucleotide polymorphisms (SNPs) in 396 protein-coding genes involved in biological processes relevant to cancer and other complex diseases, with respect to gene diversity within samples of individuals representing the three major historic human populations (African, European, and Asian) and with respect to interpopulation genetic distance. Reduced levels of both intrapopulation gene diversity and interpopulation genetic distance were seen in the case of SNPs located within the 5'-UTR and at nonsynonymous SNPs, causing radical changes to protein structure. Reduction of gene diversity at SNP loci in these categories was evidence of purifying selection acting at these sites, which in turn causes a reduction in interpopulation divergence. By contrast, a small number of SNP sites in these categories revealed unusually high genetic distances between the two most diverged populations (African and Asian); these loci may have historically been subject to divergent selection pressures.