RAPD标记在油菜隐性核不育两亲及杂种纯度检验上的应用研究(Ⅱ) -- 反应体系的优化构建

以隐性核不育双低杂交油菜黔油12号父母本及其杂交种为材料,对影响油菜RAPD分析的主要因素进行系统的比较研究,试验结果表明,25.0 μl反应体系中,最佳的组成是:10倍Buffer,2.0 mmol/L的MgCl2,0.2 mmol/L的dNTPs, 0.7 μmol/L的引物,1.5 U的TaqDNA聚合酶以及50.0 ng的模板DNA.     

利用微卫星标记分析长毛兔遗传多态性及其与产毛量相关性

利用微卫星标记技术，分析了皖系长毛兔的遗传多样性和4个微卫星座位与1岁时产毛量之间的关系。结果表明：皖系长毛兔4个微卫星座位上平均检测到4．5（3～6）个等位基因，平均杂合度为0．680（0．630-0．721），平均多态信息含量为0．642（0．559—0．705）；Sol33微卫星座位与1岁时产毛量呈显著相关（P〈0．05），其中基因型为AD和BD的个体1岁时产毛量与其他3种基因型个体间均存在显著差异（P〈0．05）；其他3个微卫星座位（Sat4、Sat13、Sol44）与1岁时产毛量相关不显著（P〉0．05）。     

Geographic isolation, genetic divergence, and ecological non-exchangeability define ESUs in a threatened sky-island rattlesnake

We utilized nine microsatellite loci and 865 bases from two mtDNA genes to estimate demographic parameters and visualize historic/contemporary connectivity among populations of a sky-island rattlesnake (New Mexico ridge-nosed rattlesnake, Crotalus willardi obscurus). This taxon is listed as threatened under the United States Endangered Species Act (ESA) and is distributed patchily within three borderland mountain ranges [Animas (ANM), Peloncillo (PEL), Sierra San Luis (SSL)] of southeastern Arizona, southwestern New Mexico and north-central México. Molecular data support a hypothesis of northward range expansion from México, with subsequent isolation on sky-islands through vicariant desertification that transformed intervening wooded valleys and low elevation passes into inhospitable habitat. Historic and recent movements have been within rather than among mountains. Although populations are linked via ancestral polymorphism, they do not represent a single mtDNA gene pool. All are genetically bottlenecked, with the Peloncillo reflecting deepest/sharpest declines and fewest captures per unit effort. Most recent population declines occurred ∼4 kybp (thousands of years before present). Thus, population reductions are historic and environmental rather than contemporary and anthropogenic. Our data demonstrate that PEL is ecologically non-exchangable with other sky-island populations, and thus comprises one ‘evolutionary significant unit’ (ESU), while SSL and ANM comprise ‘management units’ (MUs) within a second ESU. All three meet legal criteria for recognition as ‘distinct population segments’ (DPS) under the ESA.     

An integrated comparison of captive-bred and wild Atlantic salmon (Salmo salar): Implications for supportive breeding programs

Supportive breeding is a strategy consisting in maintaining a pool of locally-adapted wild genitors in captivity whose offspring are released in the wild at an early developmental stage. In this study, we tested the utility of this strategy in preventing phenotypic and genetic divergences between captive-bred and wild animals that could be detrimental for wild populations. Combining microsatellite analyses, morphological measurements and behavioural trials in the laboratory, we compared the progeny of Atlantic salmon (Salmo salar) born in captivity with individuals born in the wild. At all these levels, we found significant differences between the progeny of the two groups. Specifically, allelic frequencies significantly differed between groups, with captive-bred fish tending to be less variable with lower heterozygosity and allelic richness values. The shape of wild-born fish was also different from that of the captive-group, particularly in the depth of the head and the length of the pectoral fins. Finally, captive-bred individuals were, on average, more aggressive than wild-born fish. We demonstrated that this difference was strongly dependent upon the environment as captive-bred fish were more aggressive only when together with their wild conspecifics or with an exotic competitor, the rainbow trout (Oncorhynchus mykiss). Overall, our results showed that both phenotypic and genetic changes can arise even if genitors share a common brood-stock and after only a few months of rearing in a controlled environment. We conclude that the progeny produced in such supportive breeding programs does not meet the criteria necessary to ensure preserving the genetic and ecological integrity of wild populations.     

Genetic and bioclimatic variation in <Emphasis Type="Italic">Solanum pimpinellifolium</Emphasis>

Solanum pimpinellifolium, due to its close relationship to S. lycopersicum, has been a genetic source for many commercially important tomato traits. It is a wild species found in the coastal areas of Peru and Ecuador. In this study, the genetic variation of S. pimpinellifolium was studied using the diversity found in 10 microsatellites in 248 plants spread throughout its entire distribution area, including Ecuador, which has been underrepresented in previous studies. Peruvian and Ecuadorian accessions are genetically quite differentiated. A possible cause of these differences could be the non-uniform nature of the coastal Ecuadorian and Peruvian climates, seeing as an important correlation between genetic differentiation and climate has been found. In addition, Ecuadorian and south Peruvian accessions have a lower genetic diversity and a higher homozygosity due to their higher autogamy, lower population size, and possible colonization bottlenecks. The Galápagos Islands population is an extreme case, with no diversity, likely caused by a recent colonization from the northern continental Ecuadorian region where genetically identical plants have been found. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. Elena Zuriaga and José M. Blanca contributed equally to this work.     

Coconut (<Emphasis Type="Italic">Cocos nucifera</Emphasis> L.) DNA studies support the hypothesis of an ancient Austronesian migration from Southeast Asia to America

The centre of origin of coconut extends from Southwest Asia to Melanesia. Nevertheless, its pre-Columbian existence on the Pacific coast of America is attested. This raises questions about how, when and from where coconut reached America. Our molecular marker study relates the pre-Columbian coconuts to coconuts from the Philippines rather than to those of any other Pacific region, especially Polynesia. Such an origin rules out the possibility of natural dissemination by the sea currents. Our findings corroborate the interpretation of a complex of artefacts found in the Bahía de Caraquez (Ecuador) as related to South-East Asian cultures. Coconut thus appears to have been brought by Austronesian seafarers from the Philippines to Ecuador about 2,250 years BP. We discuss the implications of molecular evidence for assessing the possible contribution of early trans-pacific travels to and from America to the dissemination of domesticated plants and animals.     

opaque 2基因微卫星标记与玉米籽粒赖氨酸含量的关系

利用opaque2（o2）基因序列内的微卫星标记phi057、phi112和umc1066检测优质蛋白和普通玉米自交系CA335及黄早四,发现phi057是共显性标记,且具有明显的多态性。利用标记phi057对BC1F1回交群体[(CA335×黄早四)×CA335]的224个单株进行检测,两种基因型o2o2和o2O2的分离比为1︰1.24,符合孟德尔遗传分离比例。进一步将群体内     

Identification of New Resistance Loci Against Sheath Blight Disease in Rice Through Genome-Wide Association Study

Sheath blight (SB) caused by the soil borne pathogen Rhizoctonia solani is one of the most serious global rice diseases. Breeding resistant cultivar is the most economical and effective strategy to control the disease. However, no rice varieties are completely resistant to SB, and only a few reliable quantitative trait loci (QTLs) linked with SB resistance have been identified to date. In this study, we conducted a genome-wide association study (GWAS) of SB resistance using 299 varieties from the rice diversity panel 1 (RDP1) that were genotyped using 44 000 high-density single nucleotide polymorphism (SNP) markers. Through artificial inoculation, we found that only 36.5% of the tested varieties displayed resistance or moderate resistance to SB. In particular, the aromatic and aus sub-populations displayed higher SB resistance than the tropical japonica (TRJ), indica and temperate japonica sub-populations. Seven varieties showed similar resistance levels to the resistant control YSBR1. GWAS identified at least 11 SNP loci significantly associated with SB resistance in the three independent trials, leading to the identification of two reliable QTLs, qSB-3 and qSB-6, on chromosomes 3 and 6. Using favorable alleles or haplotypes of significantly associated SNP loci, we estimated that both QTLs had obvious effects on reducing SB disease severity and can be used for enhancing SB resistance, especially in improving SB resistance of TRJ sub-population rice varieties. These results provided important information and genetic materials for developing SB resistant varieties through breeding.     

四倍体野生种花生A.monticola全基因组SSR的开发与特征分析

【目的】通过对四倍体野生种花生Arachis monticola（AABB,2n = 4x = 40）全基因组SSR位点搜索,研究其全基因组SSR分布特征及规律,开发并验证其全基因组SSR引物,为花生属植物遗传进化分析及重要性状分子标记开发提供依据。【方法】在华大基因GigaScience数据库下载A.monticola全基因组序列,并利用生物信息学软件MISA进行SSR位点搜索,Primer 3进行引物设计,通过电子PCR进行单位点SSR分析,并随机合成100对SSR引物验证通用性。【结果】SSR在四倍体野生种花生A.monticola基因组上共搜索到SSR位点676 878个,平均每3.8 kb就会出现一个SSR,分布于5 127条scaffold中,单核苷酸至六核苷酸均有分布,且数量上差异较大,以单碱基、二碱基、三碱基为主,三者占SSR总数的94.28%,其中单碱基重复数量最多,占46.71％,密度最高;六核苷酸重复数目最少,分布最稀疏。大多数SSR分布在基因间区,基因区SSR多分布于内含子区域;全基因组共鉴定出395个不同的重复基元,其中A亚基因组342种,B亚基因组356种;A/T是最丰富的重复基元;在1—6个核苷酸的重复基元中,数量最多的依次是A/T、AT/AT、AAT/ATT,AAAT/ATTT、AAAAT/ATTTT、AAAAAT/ATTTTT;整体来看,重复基元的重复次数多集中在50次以内,不同类型的motif的重复次数差异很大;同一种类型重复基元的SSR位点,随着motif重复次数增加,SSR的数量逐渐降低;B03染色体上SSR数量最多,A08染色体中SSR密度最高。A.monticola全基因组SSR比A.duranensis、A.ipaensis基因组SSR数量多,密度也更高,A.monticola单核苷酸重复最丰富,2个野生种二核苷酸数量最多。共设计出SSR引物192 303对,单位点SSR标记检出率50.35%,单点SSR标记在基因组上的分布呈现两端密集,中间稀疏的特点;随机合成的100对引物中,90对能在A. monticola中扩增出稳定清晰的条带,且在4份不同的花生基因组DNA中扩增目的条带表现出不同的特点。【结论】A.monticola基因组内SSR种类和数量丰富,单核苷酸至六核苷酸均有分布,单核苷酸重复基元数量最多,且最密,六核苷酸重复基元数量最少,出现频率最低,不同重复基元频数高低与核苷酸数量没有严格相关性,SSR多分布在基因间区,基因区内含子区域SSR数量最多;A.monticola A、B亚基因组具有其各自特异的重复基元类型;单个类型重复基元数量最多的均为AT富集的重复基元,而GC富集的重复基元相对较少;同一种类型重复基元的SSR位点,随着motif重复次数增加,SSR的数量逐渐降低;A.monticola全基因组SSR较2个二倍体野生种数量更多,密度也更高且重复基元分布规律不同;经过初步验证,开发的SSR引物在4份花生材料中表现出部分通用性。     

河南地方野生小鼠遗传多样性分析

利用56个微卫星标记对河南省地方野生小鼠与4个实验室小鼠品系进行了遗传多样性分析。结果共检测出230个等位基因,平均每个位点等位基因数为4.107个,其中D4Mit9位点最多,为8个,D8Mit154、D7Mit8、D6Mit77、D17Mit244、D18Mit119位点最少,均为2个;野生小鼠基因位点平均纯合率为68.98%,除KM小鼠以外,其余实验室小鼠品系所有检测位点均为纯合;野生小鼠与PWK小鼠的平均多态性为0.657 0,与BALB/c小鼠的平均多态性为0.855 8,与B6小鼠的平均多态性为0.919 7,与KM小鼠的平均多态性为0.837 6;聚类分析结果显示,野生小鼠与PWK小鼠遗传距离最近。野生小鼠与实验室常用品系小鼠相比多态性较好,具有较高的遗传多样性和育种价值,对丰富实验小鼠基因库有着重要意义。