海陆渐渗系棉花F_2群体SSR标记偏分离的遗传分析

本研究以海陆渐渗系13-1与陆地棉辽棉12构建的F2群体为材料,利用4 500对中具有多态性的84对SSR引物进行群体间分析。研究结果显示:在p0.05显著水平上,共有19个分子标记表现偏分离,占总标记数的25.3%,其中有8个标记偏向父本辽棉12,占偏分离标记总数的42.1%;10个标记偏向母本13-1,占偏分离标记总数的52.63%;1个标记偏向杂合体,占偏分离标记总数的5.27%。这些标记在图谱上有两种分布形式,分别为成簇分布和孤立分布。在7条不同的染色体上均发现偏分离标记,其中在1染色体上发现1个热点区域。本研究分析了产生偏分离的原因,并讨论偏分离标记对QTL定位的影响。     

水稻PSM标记的发展及抗虫基因的分子定位

水稻是世界上最重要的粮食作物之一 ,为世界近一半人口提供食物来源。水稻微卫星图谱的构建有利于遗传基础的研究及分子育种。本研究通过发展位置特异性微卫星标记 ,对微卫星标记进行了图谱的整合 ,并利用微卫星等标记对水稻抗稻瘿蚊基因Gm6和抗褐飞虱基因Bph3进行了分子定位。主要研究结果如下 :1、利用网上公布的序列信息进行位置特异性微卫星引物的设计和微卫星图谱的整合。共发展了 198个PSM标记 ,有 10 5个标记的基序为GA/CT重复 ,占 5 3 3% ,绝大多数标记 (98 0 % )的重复序列长度在 2 0bp以上。将原有微卫星标记和本实验发展的PSM标记整合到RGP遗传图谱上 ,整合后总的SSR标记数为 718个 ,新图谱的遗传距离总长度为 15 2 7 2cM ,平均标记密度为每 2 13cM有一个SSR标记 ,其中第 1染色体的标记最密 (1 73cM /个 ) ,而第 11染色体的标记密度最低 (3 32cM /个 )。将本研究发展的微卫星图谱与IRMI发表的高密度微卫星进行了比较 ,结果显示本研究发展的微卫星图谱标记分布比较均匀 ,只有 3个区域标记间遗传间距在 10cM以上 ,5个区域在 8- 10cM ,而IRMI微卫星图谱分别有 17和 12个。2、采用G2 4 17- 2 - 1×抗蚊青占 (2 39株 )和G30 0 4 - 4×抗蚊青占 (2 4 3株 )两个F2 作图群体对水稻抗稻瘿蚊进行了分     

水稻野败型细胞质雄性不育恢复基因Rf3的定位

以珍汕97A/明恢63的F2群体为材料,应用SSR标记对水稻野败型恢复基因Rf3进行定位。该试验从F2分离群体中筛选出119个极端不育单株组成隐性基因定位群体。针对水稻第1染色体短臂Rf3所在染色体的可能区间,应用37个SSR标记检测亲本,从16个多态性标记中挑选出9个检测定位群体。结果表明物理位置连续排列的SSR标记RM10353、RM1195和RM3746各有8个单株与Rf3基因发生了单交换,且重组子数表现为最少,据此可将Rf3定位于这3个标记的两侧标记内。因此最终将Rf3定位在相距679.9 kb的SSR标记RM10338和RM10376之间。     

的定位

 以珍汕97A/明恢63的F2群体为材料,应用SSR标记对水稻野败型恢复基因Rf3进行定位。该试验从F2分离群体中筛选出119个极端不育单株组成隐性基因定位群体。针对水稻第1染色体短臂Rf3所在染色体的可能区间,应用37个SSR标记检测亲本,从16个多态性标记中挑选出9个检测定位群体。结果表明物理位置连续排列的SSR标记RM10353、RM1195和RM3746各有8个单株与Rf3基因发生了单交换,且重组子数表现为最少,据此可将Rf3定位于这3个标记的两侧标记内。因此最终将Rf3定位在相距679.9 kb的SSR标记RM10338和RM10376之间。     

草棉EST-SSRs的遗传评价

根据GenBank中公布的247条草棉EST序列,搜索SSR并进行引物设计。其中的25条序列含有27个SSR,1~6碱基重复类型都存在,二碱基和三碱基重复的频率较高。为了明确在A、D和AD基因组中的可转移性,依据25条序列共设计25对EST-SSR引物,其中22对引物扩增出清晰可辨的DNA条带,产生92个多态性片段,平均每对引物产生3.64个多态性片段。引物的多态性信息含量(PIC)在0.49~0.91之间,平均为0.81。6对引物在BC₁种间作图群体[(鄂棉22 × Pima3-79) ×鄂棉22]中表现多态性,产生7个多态性位点,其中5个为共显性,2个为显性。除HAU230b标记在BC₁分离群体中不符合孟德尔式分离比例,其余引物表现正常分离。6个位点被整合到陆地棉和海岛棉种间BC₁遗传连锁图谱上的6条染色体：有4个位于A亚基因组的4条染色体上(Chr.6、10、11和12),2个位于D亚基因组的2条染色体(Chr.19和20)。     

利用4个姊妹近等基因群体定位水稻粒重和粒形QTL

粒重是决定水稻产量的三要素之一。利用世界上粒重最大的品种之一SLG-1(供体亲本)与小粒品种日本晴(Nipponbare,轮回亲本)杂交,在各回交世代选择粒重较大单株与日本晴回交,构建水稻粒重和粒形的姊妹近等基因系(SNILs)。对获得的73 株BC₄F₁单株进行粒重频率分布统计,选择粒重频率分布在4个峰值处的代表性单株,自交获得4个BC₄F₂ SNILs群体。利用BSA法(分离群体分组混合分析法),从均匀分布在水稻染色体上的1 513对SSR标记中筛选出与粒重和粒形相关的多态性标记19对,以LOD≥2.5作为选择阈值,对粒重、粒长、粒宽和粒厚进行QTL扫描,共检测到6个区域的12个QTL,贡献率从7.22%到53.38%。这些QTL所在区域包含已克隆的粒长GS3和粒宽GW2,也包含没有精细定位的第2染色体的RM6318-RM1367、第3染色体的RM5477–RM6417和第6染色体的RM3370–RM1161等3个区域控制粒重和粒形的5个QTL。其中第3染色体上RM5477–RM6417区间存在粒形贡献率较大的新的QTL。构建含有这些粒重QTL的姊妹近等基因系,为进一步精细定位或克隆新的粒重或粒形QTL奠定了基础。     

基于高密度Bin图谱的水稻抽穗期QTL定位

以粳稻品种02428和籼稻品种玉针香进行杂交, 按单粒传法连续自交10代, 得到包含192个株系的重组自交系(RIL)作图群体。通过对两亲本重测序及RIL群体简化基因组测序, 构建了包含2711个Bin标记的高密度遗传图谱。该图谱各染色体标记数在162~311个之间, 标记间平均物理距离为137.68 kb。将亲本及192个株系分别于4个环境下采用随机区组种植, 并记录抽穗期。使用WinQTL Cartographer 2.5软件的CIM分析方法, 进行抽穗期相关QTL检测及定位。在4个环境下定位到影响抽穗期的QTL共14个, 分布于第1、第2、第3、第7、第8、第9和第10染色体。其中, qHD2.2和qHD10.2能在3个环境中被重复检测到, 表型贡献率分别为5.14%~11.15%和5.35%~16.97%, 分别能缩短抽穗期1.66 d和1.56 d, 具有聚合育种的应用价值。通过物理位置比对, 14个QTL中有11个与前人定位在相同或邻近区域, qHD1.1、qHD2.2和qHD9.1尚未见报道。经对qHD2.2详细分析, 在其染色体区间内找到3个与抽穗期相关的注释基因LOC_Os02g46450、LOC_Os02g46710和LOC_Os02g46940, 其中LOC_Os02g46450已被克隆。测序分析发现, 这3个基因在两亲本间都存在差异, 可作为候选基因。     

利用RIL群体对水稻再生力及相关农艺性状的QTL分析

以粳糯稻品种糯89-1与籼型重穗型杂交稻骨干恢复系蜀恢527杂交构建的籼粳交F₇代RIL群体的169个家系为作图群体,构建了一张含105个微卫星(SSR)标记的分子连锁图谱。定位了水稻正季7个农艺性状的QTL 15个,分布在第1、第2、第3、第5、第6、第7、第10染色体上,LOD值介于2.10~7.51,贡献率3.77%~25.37%,其中贡献率10.0%以上的QTL 7个,单个性状的QTL 1~4个;定位了水稻再生季7个农艺性状的QTL 19个,分布在第1、第2、第3、第4、第5、第6、第7、第10染色体上,LOD值介于2.17~18.34,贡献率3.23%~37.66%,其中贡献率10.0%以上的QTL 7个,单个性状的QTL1~5个;定位了影响水稻再生力(最终再生率)的QTL 2个(qRa4,qRa5),分别在第4和第5染色体上,贡献率分别为8.17%和7.09%,加性效应分别为0.32和-0.39,贡献率和加性效应均较小,属微效基因。共检测到两季农艺性状QTL 36个,同一性状被重复检测的QTL 8个。水稻再生力与正季稻有效穗呈极显著负相关;水稻再生力与再生稻有效穗呈极显著正相关,与每穗总粒数和着粒密度呈显著负相关。QTL定位结果揭示了有效穗是影响再生力的主要因素。     

玉米抗纹枯病QTL定位

以玉米自交系R15（抗）×掖478（感）的229个F₂单株为作图群体,构建了包含146个SSR标记位点的遗传连锁图谱,全长1 666 cM,平均图距11.4 cM。通过麦粒嵌入法对F2:4群体进行人工接种纹枯病菌,并以相对病斑高为病级划分标准鉴定了玉米纹枯病的抗性。用复合区间作图法分析抗病QTL及遗传效应,共检测到9个抗性QTL,分布于第1、2、3、4、5、6和10条染色体上,单个QTL可解释表型方差的3.72%~7.19%,其中有2个QTL位于染色体6.01抗病基因簇附近。     

陆海高代回交群体抗黄萎病QTL定位

【目的】定位棉花抗黄萎病数量性状位点(Quantitative trait loci, QTL)。【方法】以海7124和TM-1配制抗感组合F1,再以鲁棉研28为轮回亲本构建的137个BC4F1家系为作图群体,筛选出多态性重复序列(Simple sequence repeat, SSR)标记,并与已发表的整合高密度遗传连锁图谱相比对,构建遗传图谱。采用复合区间作图法(Composite interval mapping,CIM)进行大田和病圃两个环境下抗黄萎病QTL定位。【结果】216个多态性SSR位点分布在26条染色体上,可覆盖棉花基因组3 380 cM(centi Morgan),标记间平均距离15.77 cM。定位到6个QTLs,分布在6条染色体上,可解释表型变异8.56%～20.26%,其中5个QTLs与前人研究结果相一致,在第1染色体上新定位到一个QTL。本研究可为分子标记辅助选择抗病育种提供帮助。【结论】定位到6个黄萎病相关QTLs,其中1个是在第1染色体上新发现的QTL。     

棉花品种资源群体结构与连锁不平衡分析

用基因组扫描的方法,利用棉花9个连锁群上的79个微卫星标记(Simple sequence repeat,SSR),对收集的204份陆地棉品种(系)组成的品种资源群体进行群体结构和连锁不平衡(Linkage disequilibrium,LD)分析.结果表明:本研究群体可划分为3个群体,其中两个群体分别由3个亚群体组成...     

Sex-linked SSR markers in hemp

Hemp is a dioecious plant with sex chromosomes X and Y, the male sex being heterogametic. The quality of the fibre depends on the sex type. The sex chromosomes can be characterized by molecular markers. In this report, sex‐linked simple sequence repeat (SSR) markers are described. One SSR marker was polymorphic in both the populations derived from single crosses, two other markers in but one of the two populations. Three alleles were detected for two SSR markers indicating polymorphism not only between X and Y, but also between different X chromosomes. In addition, several sex‐linked RAPD markers were detected in one population. Recombination within the sex chromosomes was observed for nearly all markers.     

Quantitative trait loci mapping of freezing tolerance and photosynthetic acclimation to cold in winter two‐ and six‐rowed barley

Photoacclimation (PA) and freezing tolerance (FT) have been identified as closely related traits, due to common mechanisms of environmental control. In this study, diversity array technology (DArT) was used for identification of the quantitative trait loci (QTL) of FT and PA in winter barley. Simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers were subsequently used to saturate QTL regions. Two F₂ mapping populations were created, for two‐rowed (P44) and six‐rowed barley (CaP). Different regions of the genome were responsible for differences in traits between parents in these two populations. Eleven QTLs were identified in the P44 population, including five typical for FT and PA, on chromosomes 2H, 3H and 7H. In the CaP population, only one QTL connected with PA and 10 connected with FT were found on all chromosomes except 2H. Our results demonstrate that different sets of markers should be applied in marker‐assisted selection for FT in two‐ and six‐rowed barley, as several loci determine FT at the level of biparental crosses.     

AFLP–SSR maps of maize × teosinte and maize × maize: comparison of map length and segregation distortion

Two genetic linkage maps of Zea mays were constructed: one population comprised 94 F₂ individuals of a dent ‘B64’ × teosinte (Z. mays ssp. huehuetenangensis) cross while the second consisted of 94 F₂ individuals of a ‘B64’ × Caribbean flint ‘Na4’ cross. The level of polymorphism was higher in the ‘B64’ × teosinte combination than the ‘B64’ × ‘Na4’ combination. In the ‘B64’ × teosinte cross, a total of 338 amplified fragment length polymorphism (AFLP) and 75 simple sequence repeat (SSR) markers were mapped to 10 chromosomes, which covered 1402.4 cM. In the ‘B64’ × ‘Na4’ cross, a total of 340 AFLP and 97 SSR markers were mapped to 10 chromosomes, covering 1662.8 cM. Segregation distortion regions were found on chromosomes 4, 5 and 8 in the ‘B64’ × teosinte cross and on chromosome 9 in the ‘B64’ × ‘Na4’ cross. Comparison of the two maps revealed that the maize × teosinte map was 11.5% shorter than the maize × maize map. The maps generated in this study may be useful to identify genes controlling flooding tolerance.     

Association analysis using SSR markers to find QTL for seed protein content in soybean

Association analysis studies can be used to test for associations between molecular markers and quantitative trait loci (QTL). In this study, a genome-wide scan was performed using 150 simple sequence repeat (SSR) markers to identify QTL associated with seed protein content in soybean. The initial mapping population consisted of two subpopulations of 48 germplasm accessions each, with high or low protein levels based on data from the USDA’s Germplasm Resources Information Network website. Intrachromosomal LD extended up to 50 cM with r ² > 0.1 and 10 cM with r ² > 0.2 across the accessions. An association map consisting of 150 markers was constructed on the basis of differences in allele frequency distributions between the two subpopulations. Eleven putative QTL were identified on the basis of highly significant markers. Nine of these are in regions where protein QTL have been mapped, but the genomic regions containing Satt431 on LG J and Satt551 on LG M have not been reported in previous linkage mapping studies. Furthermore, these new putative protein QTL do not map near any QTL known to affect maturity. Since biased population structure was known to exist in the original association analysis population, association analyses were also conducted on two similar but independent confirmation populations. Satt431 and Satt551 were also significant in those analyses. These results suggest that our association analysis approach could be a useful alternative to linkage mapping for the identification of unreported regions of the soybean genome containing putative QTL.     

Molecular characterization of the recombinant inbred line population derived from a japonica-indica rice cross

Recombinant inbred line (RIL) populations of rice are useful genetic sources for map-based cloning of agronomically important genes. Zhe733 is a high-yielding indica cultivar from China conferring resistance to rice blast (RB), rice water weevil (RWW) and straighthead; whereas Kaybonnet low-phytic acid 1-1 (KBNTlpa) is a mutant of a tropical japonica cultivar from the US containing low-phytic acid with average yield, and is susceptible to some RB races, RWW, and straighthead. A 355 RIL F₁₀₋₁₁ population derived from the cross of KBNTlpa × Zhe733 was recently released. Simple sequence repeat (SSR) markers were used to evaluate 269 RILs of this population. A total of 107 polymorphic markers were mapped on all rice chromosomes representing a total of 1,016.3 cM of genetic distance. Two hundred and thirty-five KBNTlpa × Zhe733 RILs (KZRILs) were clustered into seven groups based on allele frequencies of SSR markers. Twenty-three markers (21.1%) on chromosomes 3, 6, 7, 9, and 11 were found to favor Zhe733 (χ ² = 16.8−189.7 and P < 0.01) and five markers (4.6%) on chromosome 1 and 6 were found to favor KBNTlpa (χ ² = 18.5−46.6 and P < 0.01). Marker segregations were observed to be normal for both parents except 26 (10.2%) KZRILs were found to skew toward Zhe733 (χ ² > 15.7 and P < 0.01). Furthermore, the average frequencies of heterozygosity and non-parental alleles per KZRIL were 1.3% (0.0−38.9%) and 0.4% (0.0−15.0%), respectively. Thirteen heterozygous KZRILs were found at more than five markers loci and nine KZRILs were found with more than five non-parental alleles representing 5.1 and 3.5% of 255 KZRILs. Overall, this KZRIL population is a good population with relatively low frequencies of heterozygosity and non-parental alleles, and with relatively low percentages of skewed markers and skewed KZRILs. The profiles of these SSR markers should facilitate molecular tagging critical genes controlling yield, RB, RWW, and straighthead resistance.     

Identification of population-specific QTLs for flowering in soybean

Flowering is an important stage in plant development and crucial for adaptation of plant species to different environments. Two soybean mapping populations were used to identify quantitative trait loci (QTLs) for days to flowering (DF) and days to maturity (DM) by genotyping simple sequence repeat (SSR) markers. Single-factor analysis of variance detected association of phenotypic data with SSR markers in each population. DF QTLs were identified on four chromosomes (chrs.); two QTLs located on chrs. 2 and 13 with Satt041 and Satt206 in the Jinpumkong 2 × SS2-2 population and other two DF QTLs were detected on chrs. 6 and 19 with Satt100 and Satt373 in the Iksannamulkong × SS2-2 population. The major QTLs associated with Satt100 explained 30.3% of maximum phenotypic variation. Especially, all DF QTLs included QTLs for DM, except Satt206 on chr. 13. Moreover, two additional DM QTLs were mapped on chrs. 10 and 11 with Satt243 and Satt359, respectively. DF QTL on chr. 2 with Satt041 was the newly identified QTL only in the Jinpumkong 2 × SS2-2 population and explained 10.3% of the phenotypic variation. The single locus of Satt100 on chr. 6 and Satt373 on chr. 19 were located on soybean genomic regions of the known flowering gene loci E1 and E3, respectively. These population-specific QTLs (Satt100 and Satt373) are the major QTLs for flowering time, putatively, they may be related to maturity QTLs with large effect. Additionally, these QTLs are valuable for marker-assisted approaches and could be widely adopted by soybean breeders.     

Transferability of rice SSR markers to bamboo

Simple sequence repeat (SSR) markers are widely applied in studies of plant molecular genetics due to their abundance in the genome, codominant nature, high repeatability, and transferability in cross-species applications. To investigate the possibility of applying rice SSR markers in bamboo, we selected 120 rice SSR markers that are evenly distributed on rice chromosomes and assessed these for their transferability to 21 different bamboo species. A total of 4847 bands of 2196 alleles were obtained from 82 SSR markers that were able to amplify products in the bamboo genome; the transferability was 68.3%. Seven markers specifically amplified individual bamboo species and are consequently valuable markers for species identification. SSR markers located on rice chromosome 7 and 1 showed the highest and lowest transferability, respectively to the bamboo genome. SSR markers located on some regions of the rice chromosomes could not be amplified in bamboo, suggesting that regional divergence occurred between rice and bamboo during evolution. A dendrogram was constructed. The dendrogram classified bamboo species into two major groups which coincided with rhizome type, runner, and clumper. The results of this study demonstrate that rice SSR markers can be a valuable source of markers for those genomes lacking useful marker systems.     

小麦分子遗传图谱的加密

高密度的分子标记遗传图谱是QTL定位、图位克隆和分子标记辅助选择等研究的基础。以小麦品种“京花1号/小白冬麦”的双单倍体(DH)群体和“农大015/复壮30”的重组自交系(RIL)群体为作图群体,选用在DH群体双亲间的339个多态性标记和在RIL群体双亲间的343个多态性标记分析作图群体各个株系的基因型,对本中心近年开发的SCAR、EST-SSR标记以及他人开发的SSR、EST-SSR标记进行了染色体定位,并利用连锁分析软件Joinmap 4.0将2个作图群体的结果整合,最终构建了10个连锁群,将217个SSR、EST-SSR和SCAR位点定位在9条染色体上,进一步提高了小麦遗传图谱的密度。     

QTLs for Fusarium head blight response in a wheat DH population of Wangshuibai/Alondra‘s’

Summary A doubled haploid (DH) wheat population derived from the cross Wangshuibai/Alondra‘s’ was developed through chromosome doubling of haploids generated by anther culture of hybrids. Fusarium head blight (FHB) was evaluated for three years from 2001 to 2003 in Jianyang, Fujian Province, China, where epidemics of FHB have been consistently severe. After 307 pairs of simple sequence repeat (SSR) primers were screened, 110 pairs were polymorphic between Wangshuibai and Alondra`s’, and used to construct a genetic linkage map for detection of quantitative trait loci (QTLs). A stable QTL for low FHB severity was detected on chromosomes 3B over all three years, and QTLs on chromosomes 5B, 2D, and 7A were detected over two years. Additional QTLs on chromosomes 3A, 3D, 4B, 5A, 5D, 6B and 7B showed marginal significance in only one year. Six QTLs were detected when phenotypic data from three years were combined. In addition, significant additive-by-additive epistasis was detected for a QTL on 6A although its additive effect was not significant. Additive effects (A) and additive-by-additive epistasis (AA) explained a major portion of the phenotypic variation (76.5%) for FHB response. Xgwm533-3B and Xgwm335-5B were the closest markers to QTLs, and have potential to be used as selectable markers for marker-assisted selection (MAS) in wheat breeding programs.