Genetic consequences of animal translocations: A case study using the field cricket, Gryllus campestris L.

Animal relocations have become a common tool in nature conservation, but the genetic consequences of such projects have rarely been studied in insects. As both natural and artificial formation of new populations may lead to genetic drift (founder effect), decreased genetic diversity and increased rates of inbreeding, genetic analyses can provide valuable information to evaluate the success of a relocation project. The field cricket (Gryllus campestris) has been subjected to reintroduction and translocation projects in England and northern Germany. Here, we present a microsatellite study on the population genetics of one recently established population of this species in comparison with several older populations and some recently colonized sites. Our results show that the translocation did not result in a significant loss of genetic diversity, when compared to source and other natural populations suggesting that translocation of a high number of nymphs from different subpopulations may be a suitable method to decrease the loss of genetic diversity and reduce the risk of inbreeding. Furthermore, the translocation had no negative effect on the source population, which reached a new maximum population size in 2006. An assignment test showed that individuals from the translocated population (F4 generation) were still assigned to the source populations, whereas two young subpopulations that originated by natural colonization from the central population about ten years ago already formed separate genetic clusters. As the strong fragmentation of G. campestris populations in northern Germany hampers natural colonization of newly created potential habitats, translocation projects seem to be an appropriate method to preserve this species.     

Evaluation of genetic diversity and relationships within an on-farm collection of Perilla frutescens (L.) Britt. using microsatellite markers

The present study demonstrates utilization of 11 microsatellite markers to explore genetic diversity held in Perilla frutescens (L.) Britt. landrace accessions growing on farms in different parts of Korea and Japan and to assess their genetic relationships. All microsatellite loci were polymorphic and produced a total of 96 alleles ranging from 4 to 20, with an average of 8.7 alleles per locus. Of the 96 alleles found, a total of 15 unique landrace-specific alleles were observed at 9 different loci. The locus GBPFM203 provided the highest number of alleles (20), of which five were unique and each specific to a particular landrace accession. The occurrence of unique, accession-specific alleles presented molecular evidence for the generation of new alleles within on-farm collection of Perilla. The mean values of observed (H _O) and expected heterozygosity (H _E) were 0.39 and 0.68, respectively, indicating a considerable amount of polymorphism within this collection. A genetic distance-based phylogeny grouped the two Perilla varieties, var. frutescens and var. crispa (Thunb.) Decne into two distinct groups. Accessions belonging to var. frutescens could also be divided into two subgroups at a close genetic distance (GD = 0.432). The overall clustering pattern did not strictly follow the grouping of accessions according to their geographic origins. These observations are indicative of extensive germplasm exchange among farms from different geographical regions. The genetic similarity observed among the Perilla landraces may be useful for future Perilla crop variety identification, conservation, and improvement programs.     

盐胁迫下水稻幼苗存活率的QTL定位

盐胁迫是制约水稻产量的重要非生物胁迫因素。随着土壤盐碱化日益加重,培育适宜于盐碱地种植的水稻耐盐新品种是提高水稻产量的有效方法。相较于传统杂交育种,分子标记辅助育种能够提高选育的效率和精确度。选择高度耐盐籼型恢复系ST1050和盐敏感优质粳稻品种越光作为研究材料,用含有150 mmol/L Na Cl的营养液处理三叶期幼苗1周,再用普通营养液恢复处理1周后,以幼苗的存活率作为苗期耐盐指标,选取均匀分布于水稻染色体的463个SSR标记对亲本进行多态性分析,鉴定ST1050与越光杂交产生的F2代群体基因型,构建遗传图谱并进行QTL定位。结果显示,籼型恢复系ST1050、粳稻品种越光的存活率分别为60%和18.75%,差异显著。463个SSR标记中有121个在ST1050和越光之间表现出较好的共显性差异,多态性达26.13%。利用软件Ici Mapping 4.1分析ST1050×越光138个F2个体的基因型,最终获得了一张覆盖总遗传距离为1 160.09 c M,标记间平均距离9.59 c M的遗传图谱。结合F3代群体在盐胁迫后的存活率验证,在水稻8号、12号染色体上分别检测到1个苗期耐盐QTL,命名为q SR-8和q SR-12,贡献率分别为13.57%和6.91%。研究表明,籼型恢复系ST1050存在2个苗期耐盐QTL,对提高水稻的耐盐性发挥重要的作用,可以作为苗期耐盐供体用于标记辅助选择耐盐育种。     

宁春4号与河东乌麦杂交F2代抗病性及分子标记鉴定

为给宁夏小麦抗病育种提供优异资源,以宁春4号、河东乌麦及其杂交F₂代331个单株为材料,进行了群体抗病性与分子标记鉴定。结果表明:宁春4号中感白粉病、条锈病和叶锈病,河东乌麦中抗至高抗白粉病、中抗条锈病和叶锈病。在F₂代分别鉴定出68、54、52个单株抗白粉病、条锈病、叶锈病,比例依次为20.54%、16.32%、15.71%,其中,50个单株同时抗白粉病和条锈病,44个抗白粉病和叶锈病,32个抗条锈病和叶锈病,29个抗白粉病、条锈病和叶锈病。在F₂代群体中检测到239个单株携带Pm16基因,22.59%携带该基因的单株表现田间抗白粉病;202个携带Yr2基因,16.83%携带该基因的单株抗条锈病;246个携带Lr24,17.07%携带该基因的单株抗条锈病;148个单株同时携带基因Pm16和Yr2,185个单株同时携带基因Pm16和Lr24,155个单株同时携带基因Yr2和Lr24,119个单株同时携带基因Pm16、Yr2和Lr24。新开发的6个SSR标记共检测到10个抗病性数量性状基因座(QTL),涉及2A、5A、3B、5D等4条染色体,加性效应为-0.15~0.08,对表型贡献率为2%~4%,连锁系数(LOD值)最大为10.40,其中,5A、3B和5D染色体存在抗病的QTL富集区。     

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。     

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.     

白唇鹿的微卫星遗传多态性分析

为科学评价、保护和利用白唇鹿资源,采用微卫星DNA标记技术,从牛微卫星引物中筛选出13对引物对38头白唇鹿进行遗传多样性分析。结果显示,共检测到39个等位基因,其中位点RT1、RT13、CSSM19呈单态性;其余10个位点中,多态信息含量(PIC)和杂合度(He)分别为0.049 9～0.652 6,0.051 9～0.702 8,白唇鹿群体的平均PIC为0.320 2,平均期望He为0.396 5。Shannon信息指数(I)为0.121 7～1.369 3,平均为0.694 2。位点NVHRT48的3项指标都最大,说明其变异水平最高,具有明显的遗传优势。3项指标都表明白唇鹿群体属于中度多态性,应加以重点保护和合理利用。研究结果进一步验证了PIC与He的相关性。     

胡桃EST-SSR标记的筛选及引物设计

[目的]筛选胡桃的EST-SSR分子标记并对其进行引物设计。[方法]利用生物信息学方法对NCBI网上公开的5213条胡桃（Juglans regia Linn.）ESTs序列进行EST-SSR特征分析,利用利用Primer3.0软件对筛选出的EST序列设计引物。[结果]在ESTs序列中共检索出207个SSR,其中无冗余序列188,检出率为3.97%,平均分布距离为21.12kb,包括92种重复基元,其中以二核苷酸和三核苷酸重复类型为主,分别占总数目的31.40%和35.27%;对随机筛选出的50条SSR引物进行PCR扩增验证,初步筛选出30对引物。[结论]通过对胡桃EST序列中SSR位点的发掘分析,有针对性地设计EST-SSR引物,将为胡桃科EST-SSR分子标记的开发奠定基础。     

不同生态地点下稻米外观品质性状的QTL定位分析

 利用两个已测序品种93 11和日本晴为亲本,采取单粒传法创建由190个家系组成的重组自交系群体,并构建了包含178个SSR、CAP和STS标记的遗传连锁图谱。采用复合区间作图方法,在3个不同生态地点(陵水、合肥和怀远)对垩白(垩白率、垩白大小、垩白度)、粒形(粒长、粒宽、长宽比)等6个外观品质的数量性状基因座（QTL)进行了定位分析。共定位到39个QTL,单个性状QTL数目在6~7个,说明垩白和粒形是多基因控制的数量性状。8个QTL可在2个以上地点检测到,其中,两个垩白度相关QTL qCD 1、qCD 3(贡献率分别为288%、321%)在3个地点同时检测到;11个QTL具有一因多效性,单个QTL位点控制的性状为2~6个,如第3染色体RM16-RM143区段控制垩白率、垩白大小、垩白度、粒长、粒宽和长宽比等6个性状。比较3个地点的检测结果,发现外观品质性状的QTL定位都受环境影响,但不同性状受影响的程度不同。长宽比和垩白度受环境影响较小,粒宽受环境影响较大。     

利用重测序的染色体片段代换系群体定位水稻粒型QTL

 以一套用籼稻品种9311为受体、粳稻品种日本晴为供体构建的128个染色体片段代换系为材料,按随机区组实验设计种植,于成熟后考查代换系粒长、粒宽性状,利用多元回归分析方法,结合Bin图谱,鉴定出6个与粒长相关的QTL、2个与粒宽相关的QTL。其中,qGL3.1被定位在水稻第3染色体的5 792 954 bp区间内;qGL3.2被定位在第3染色体的917 878 bp区间内;qGL8.1被定位在第8染色体的889 543 bp区间内;qGL8.2被定位在第8染色体的208 614 bp区间内;qGL9.1被定位在第9染色体的1 149 685 bp区间内;qGL11.1被定位在第11染色体的3 184 760 bp区间内;qGW1.1被定位在第1染色体的200 070 bp区间内;qGW5.1被定位在第5染色体的704 905 bp区间内。上述QTL的准确定位,为进一步精细定位及克隆相应QTL和开展水稻粒型分子育种奠定了基础。