Population Genetic Diversity in Chinese Pomegranate (Punica granatum L.) Cultivars Revealed by Fluorescent-AFLP Markers

Eighty-five pomegranate （Punica granatum L.） cultivars from six geographical populations located at Shandong, Anhui, Shaanxi, Henan, Yunnan, and Xinjiang Provinces were studied for its population genetic diversity by means of fluorescent-AFLP markers. The results indicated that 135-185 polymorphic loci were amplified by eight pairs of primers at species level. An average of 158.25 polymorphic loci was amplified for each primer combination. The polymorphism percentage ranged from 62.5% to 86.11%, and the average polymorphism percentage was 73.26%. This indicated that there was plentiful genetic diversity in pomegranate cultivars. The genetic diversity at the species level was higher than that at the population level. The order of the genetic diversity was Henan population 〉 Xinjiang population 〉 Shaanxi population 〉 Anhui population 〉 Shandong population 〉 Yunnan population. Variance analysis showed that there was significant difference between populations in genetic diversity. The genetic differentiation coefficient between populations （Gsr） was 0.2018, which indicated that gene differentiation was mainly within the population, and between populations, it accounted for 20.18% of the total variation. Gene flow （Nm） between the populations measured was 1.9027 based on the genetic differentiation coefficient between populations, indicating that there was mild gene flow between populations. The UPGMA cluster analysis showed that most accessions from the same population were clustered together, but there was partly gene exchange. All genetic parameters indicated that there was plentiful genetic diversity in pomegranate cultivars in China, of which Henan population was significantly higher than the other populations, and it had wide application foreground in pomegranate breeding in China.

Population Genetic Structure in Apricot (Prunus armeniaca L.) Cultivars Revealed by Fluorescent-AFLP Markers in Southern Xinjiang,China

Population-wide genetic structure was studied using fluorescent-AFLP markers on 85 apricot （Prunus armeniaca L.） cultivars collected from Kuche, Kashi, Hetian in the Tarim Basin, southern Xinjiang Uygur Autonomous Region of China. The purpose of this study was to determine the genetic structure and genotypic diversity among the different eco-geographical populations. Based on the results from this study, 8 pairs of fluorescent-AFLP primers showed clear electrophoregram and high polymorphism amongst the 64 pairs of EcoR Ⅰ/Mse Ⅰ （Mse Ⅰ - a FAM fluorescent marked primer） primers screened. There was a significant polymorphic difference for the same primer pair in different populations and for the same population with different primer pairs. The percentage of polymorphic loci （P） at species level was higher than Kuche, Hetian, Kashi population levels, respectively. The Nei＇s gene diversity index （H） and Shannon＇s information index （I） at species level were higher than those of Kuche, Hetian, and Kashi at population level, respectively. H and I of Kuche population were the highest amongst the three populations. Apricot population genetic diversity was found mainly within the population, Genetic differentiation coefficient between populations （GST） was 0.0882. Gene flow Nm between the populations was 5.1689. Population genetic identity was between 0.9772-0.9811 and genetic distance was between 0.0191-0.0232. These results further indicated that the similarity between populations was higher and the genetic distance between populations was smaller. The UPGMA cluster analysis indicates that the geographical populations at Kuche, Kashi, Hetian were relatively independent Mendelian populations. Concurrently, there was also partial gene exchange between the populations. All the evidences indicated that the genetic diversity in Kuche population was the highest, suggesting that it could be a transition population from wild apricot to cultivated apricot. There were abundant genetic diversities in apricot cultivar populations in southern Xinjiang, China, which provide promising germplasm for further breeding and theoretical basis for biodiversity conservation and utilization for apricot population in this area.

AFLP Marker Linked to Turnip Mosaic Virus Susceptible Gene in Chinese Cabbage(Brassica rapa L.ssp.pekinensis)

Turnip mosaic virus (TuMV) which has several strains causes the most important virusdisease in Chinese cabbage in terms of crop damage. In China, Chinese cabbage is infectedby a mixture of strains, breeding of cultivar for the TuMV resistance has become themajor aim. Screening the molecular marker linked to the TuMV-resistance gene formolecular assisted selection is the major method to improve the breeding efficiency. Inthis study, we used AFLP technique and the method of bulked segregant analysis(BSA) tostudy the progeny of Brp0058Brp0108, and identified two DNA molecular marker linked toTurnip mosaic virus-resistance gene with a recombination frequency 7.5 cM and 8.4 cM.

Application of AFLP markers for population genetic study on half-smooth tongue sole Cynoglossus semilaevis

The genetic diversity of wild and hatchery populations of half-smooth tongue sole Cynoglossus semilaevis, based on observation of amplified fragment length polymorphism (AFLP) was described. Two hundred individuals from four wild populations, Laizhou (LZ), Weihai (WH), Qingdao (QD), Rizhao (RZ), and one hatchery population, Mingbo (MB), were screened using eight different AFLP primer combinations. A total of 384 loci were screened in the five studied populations. 48.4%, 51.3%, 50.7%, 49.3% and 45.8% of these loci were polymorphic among the individuals tested in the LZ, WH, QD, RZ and MB populations, respectively. The number of polymorphic loci detected by single primer combinations ranged from 17 to 35. The average heterozygosity of the LZ, WH, QD, RZ and MB populations was 0.072, 0.093, 0.092, 0.090 and 0.063, respectively. The WH population showed the highest genetic diversity in terms of total number of AFLP bands, total number of polymorphic bands, average heterozygosity and percentage of low frequency (0-0.2) polymorphic loci among all the populations, while the LZ population was the lowest among the wild populations. Compared with the wild populations, the hatchery population showed a low genetic viability.

Genetic Analysis of Floating Enteromorpha prolifera in the Yellow Sea with AFLP Marker

Extremely large accumulation of green algae Enteromorpha prolifera floated along China'coastal region of the Yellow Sea ever since the summer of 2008.Amplified Fragment Length Polymorphism (AFLP) analysis was applied to assess the genetic diversity and relationships among E. prolifera samples collected from 9 affected areas of the Yellow Sea.Two hundred reproducible fragments were generated with 8 AFLP primer combinations,of which 194 (97%) were polymorphic. The average Nei's genetic diversity, the coefficiency of genetic differentiation (Gst), and the average gene flow estimated from Gst in the 9 populations were 0.4018, 0.6404 and 0.2807 respectively. Cluster analysis based on the unweighed pair group method with arithmetic averages (UPGMA) showed that the genetic relationships within one population or among different populations were all related to their collecting locations and sampling time. Large genetic differentiation was detected among the populations.The E. prolifera originated from different areas and were undergoing a course of mixing.

QTL Mapping for Fiber Quality Traits Based on a Dense Genetic Linkage Map with SSR,TRAP,SRAP and AFLP Markers in Cultivated Tetraploid Cotton

Cotton is one of the most important economic crops in the world,and it provides natural fiber for the textile industry.With the advancement of the textile technology and increased consumption demands on cotton fiber,both cotton yield and quality should be enhanced.However,cotton yield

Genetic Diversity Within a Jackfruit (Artocarpus heterophyllus Lam.) Germplasm Collection in China Using AFLP Markers

Jackfruit is cross-pollinated and mostly seed propagated, a wide range of variation exists in fruit quality. With the development of efficient vegetative propagation methods, excellent genotypes selected from these seed propagated seedlings will gradually replace other genotypes in jackfruit producing areas. In this study, genetic diversity of 50 jackfruit accessions from three provinces in China was analyzed based on amplified fragment length polymorphic （AFLP） markers. A total of 320 unambiguous bands were produced by eight primer combinations, and 65 （20.3%） of them were polymorphic. Genetic similarity coefficients ranged from 0 to 0.9841, with an average of 0.5000, indicating a moderate genetic diversity in this collection. The dendrogram derived by unweighted pair group method with arithmetic mean algorithm （UPGMA） analysis revealed five groups, and no correlation between genetic relationship and geographical origin were found. Accessions of soft and firm flesh type were not clustered into distinct groups, neither could yearly bearing once, or twice fruit accessions. This study has provided useful information for collection and preservation of jackfruit germplasm worldwide.

Inheritance of Powdery Mildew Resistance in Cucumber (Cucumis sativus L.) and Development of an AFLP Marker for Resistance Detection

Cucumber powdery mildew is one of the most destructive diseases of cucumber throughout the world. In the present study, inheritance of powdery mildew resistance in three crosses, and linkage of resistance with amplified fragment length polymorphism （AFLP） markers are studied to formulate efficient strategies for breeding cultivars resistant to powdery mildew. The joint analysis of multiple generations and AFLP technique has been applied in this study. The best model is the one with two major genes, additive, dominant, and epistatic effects, plus polygenes with additive, dominant, and epistatic effects （E-l-0 model）. The heritabilities of the major genes varied from 64.26% to 97.82%, and susceptibility was incompletely dominant for the two major genes in the three crosses studied. The additive effects of the two major genes and the dominant effect of the second major gene were high, and the epistatic effect of the additive-dominant between the two major genes was the highest in cross I . In cross II, the absolute value of the additive effect, dominant effect, and potential ratio of the first major gene were far higher than those of the second major gene, and the epistatic effect of the additive-additive was the highest. The genetic parameters of the two major genes in cross III were similar to those in cross II. Correlation and regression analyses showed that marker E25/M63-103 was linked to a susceptible gene controlling powdery mildew resistance. The marker could account for 19.98% of the phenotypic variation. When the marker was tested on a diverse set of 29 cucumber lines, the correlation between phenotype and genotype was not significant, which suggested cultivar specialty of gene expression or different methods of resistance to powdery mildew. The target DNA fragment was 103 bp in length, and only a small part was found to be homologous to DNA in the other species evaluated, which indicated that it was unique to the cucumber genome.

Identification of AFLP Markers Linked to Lr19 Resistance to Wheat Leaf Rust

AFLP analyses were carried out on Thatcher, 23 near-isogenic lines and F2 generation of TcLr19 × Thatcher, to develop molecular markers for gene Lr19 resistance to wheat leaf rust. Seven markers linked to Lr19 resistance trait were obtained, which were P-AGT/M-GAG289 bp （3.3 cM）, P-ACA/M-GGT102 bp （4.1 cM）, P-ACA/M-GGT106 bp （4.1 cM）, P-AAC/M-CAG123 bp （4.9 cM）, P-AAC/M-GGT203bp （5.0 cM）, P-ACA/M-GGT290bp （5.7 cM）, and P-ATC/M-GAG293bp （9.6 cM）. All of these specific fragments were isolated from the polyacrylamide gels, reamplified, cloned, and sequenced. The research may facilitate genetic mapping, physical mapping, and the eventual cloning of Lr19.

Evaluation of Genetic Diversity in Wild Diploid Wheat Triticum boeoticum from Iran Using AFLP Markers

Although Iran is a main center of distribution of wild wheats, but little information is available regarding genetic variation in wild wheat relatives from this country (Tabatabaei and Massoumi, 2001). The habitats of

AFLP and SCAR Markers Associated with Peel Color in Eggplant (Solanum melongena)

Peel color is an important breeding objective for eggplant. Dark purple and purplish red are the most common colors in commercial eggplant cultivars. A co-dominant amplified fragment length polymorphism （AFLP） marker which was associated with the peel color （each in coupling phase to dark purple and purplish red） was found in studying the genetic diversity in 58 eggplant accessions （contained cultivars and wild relatives）. The maker bands were sequenced and converted to SCAR marker, this polymorphism in sequence was from an inserted/deleted （indels） mutation. And DNA from 136 eggplant materials （inbred lines, F1, and wild relatives） were amplified with the designed SCAR primers as template, high correlation between the SCAR marker and peel color （dark purple and purplish red） was found. Then, bulked line analysis （BLA） combined with AFLP was further used to identify polymorphic fragments, and another six AFLP markers were tested and verified to be associated with peel color, which demonstrated that BLA was an useful method for identifying molecular markers of interested traits. In conclusion, these markers will facilitate the MAS （maker-assisted selection） of eggplant breeding for peel color.

The Genetic Relationship of Two New Colorful Sweet Osmanthus fragrans Cultivars Revealed by AFLP and SSR Markers

Osmanthus fragrans is well-known as an ornamental and agricultural plant noted for its unique fragrance.We investigated the genetic relationships between two new colorful O.fragrans cultivars,Ziyan Gongzhu and Qiannan Guifei,and their relationships with other O.fragrans using amplified fragment length polymorphism(AFLP)and simple sequence repeat(SSR),compared to the Changye Muxi species.55 AFLP primer pairs and 17 SSRs were screened;1103 and 45 amplification products were produced,of which 92.29%of the AFLP and 62.20%of the SSRs were polymorphic.At the population level,the number of effective alleles varied from 0.76 to 1.11,and the Shannon index(I)ranged from 0 to 0.11,indicating a narrow genetic base of O.fragrans cultivars.The genetic similarity varied from 0.61 to 0.80 between Ziyan Gongzhu and other O.fragrans cultivars,and 0.57 to 0.67 in the Qiannan Guifei and other cultivars.The unweighted pair group method with arithmetic mean(UPGMA)clustering revealed that Ziyan Gongzhu may belong to the O.fragrans Albus group.However,the Qiannan Guifei cultivar was clustered into a group,showing that it has great genetic variation.These results provide new molecular evidence for germplasm resources protection,and new cultivars for breeding.

AFLP Molecular Markers for Leaf Rust Resistance Genes in Foxtail Millet

Foxtail millet is not only a very useful experimental crop, but also a fodder crop and a staple food of people who live on the marginal agricultural lands, and it supplies high-quality protein for food products and industrial materials. However, leaf rust greatly reduces foxtail millet yields in susceptible varieties when weather conditions favor rust spread and development. Therefore, it is necessary to use molecular markers detecting and marking resistance genes. Compared with other molecular markers, AFLP maker is more efficient and powerful in the study of foxtail millet. In this study, AFLP analysis of 131 F2 individuals was performed and three AFLP makers were found to be linked to the rust resistance gene, with the genetic distances of 9.2, 9.8 and 12.4 cM, respectively. Cloning of rust re- sistance genes is of great importance and meaning in studying rust resistance of foxtail millet in the future. Furthermore, we may convert specific AFLP markers into single locus PCR markers, such as sequence characterised amplified region （SCAR） markers or cleaved amplified polymorphic site （CAPS） markers.

Identification of an AFLP marker linked to the stripe rust resistance gene Yr10 in wheat

AFLP analysis of near-isogenic lines of the stripe rust resistance gene Yr10 was carried out with 6 Pst I -primers and 10 Taq I -primers with the donor parent of Yr1O gene as the check. A total of about 4200 distinguishable bands were amplified, of which 5 were stable. The genetic linkage of the 5 polymorphic DNA fragments with the target gene were tested preliminarily on a segregating F2 population derived from a cross between the gene donor parent 'Moro' and susceptible cultivar 'Mingxian 169'. The DNA fragment PT0502 was found closely linked to the Yr10 gene and cloned and sequenced. Based on the sequence specific primers for PCR were designed and synthesized. Genetic linkage analysis with 195 segregating F2 plants indicated that the genetic distance was 0.5 cM between the main product SC200 fragment produced by PCR with the primers and the Yr10 gene. The primers can be used to detect the Yr10 gene quickly, effectively and exactly.

Genetic differentiation of Helicoverpa armigera （Hübner） and H. assulta （Guenée） （Lepidoptera： Noctuidae） based on AFLP markers

Here we use amplified fragment length polymorphism （AFLP） to assess genetic differentiation of Helicoverpa armigera and H. assulta. The results indicated that both species-specific fingerprints and cluster analysis showed the ability of AFLP technique to discriminate the two sibling species; among a total 1963 AFLP markers amplified from nine primer combinations： 777 （39.6%） were H. armigera-specific, 602 （30.7%） were H. assulta- specific, and 584 （29.7%） were common bands. The mean number ofH. armigera-specific bands was significantly more than that of H. assulta-specific bands for nine primer combinations （P 〈 0.05）; the intraspecific distance of H. armigera and H. assulta was 0.123 0 and 0.110 7 respectively, and the interspecific distance was 0.178 3. In addition, the percentage of polymorphic loci and estimated average heterozygosity were used to estimate genetic diversity of the two species. This study therefore demonstrates that AFLP analysis is a sensitive and reliable technique to study genetic differentiation and genetic relationships between species and provides sufficient molecular markers for future linkage map conslruction, location and eventual cloning of genes involved in traits differentiation.

Genetic Diversity within Wild Potato Species (Solanum spp.) Revealed by AFLP and SCAR Markers

Exploitation of variability displayed by wild Solanum species for breeding the cultivated potato (S. tuberosum) requires phenotypic and genotypic characterization of germplasm resources. In the present work, a collection of 15 wild Solanum species was investigated for resistance to pathotype Ro2 of the nematode Globodera rostochiensis. Most of the genotypes reduced reproduction of the nematode, compared to the control variety Spunta, a highly resistant genotype being an accession of S. tuberosum spp. andigena. The genetic variability of the Gro1 gene cluster, which confers resistance to some pathotypes of G. rostochiensis, was then studied in the Solanum species used in this study. For this purpose, SCAR markers for eight paralogues of Gro1 gene were developed. No species showed the same pattern of the resistant control genotype. Moreover, wide-genome variability was also assessed by using AFLP markers, which allowed species-specific markers to be identified for each genotype analyzed.

大白菜中与芜菁花叶病毒(TuMV)感病基因连锁的AFLP标记

TuMV是大白菜病毒病的主要病原物之一,所以抗TuMV病毒病成为白菜抗病育种的主要目标,寻找与抗性基因紧密连锁的分子标记,进行分子标记辅助育种,是提高白菜抗病育种效率的有效手段。以抗病自交系Brp0058和感病自交系Brp0181杂交后代的F2分离群体为试材,采用分离群体分组分析法(BSA),筛选到2个与TuMV感病基因紧密连锁的AFLP分子标记,利用MAPMAKER/EXP(Version3.0)作图软件统计,其遗传距离分别为7.5和8.4cM。

野败型杂交水稻恢复基因的AFLP标记研究

选择汕优６３ Ｆ_２的高可育株和高不育株分别建立 ２个基因池，利用 ＡＦＬＰ标记技术对 ２ 池间的多态性进行了研究。分析表明，６４组引物在两池间全部扩增出了稳定、清晰的带纹，共 计３ ４７７条带。多数引物在基因池间未呈现多态性，只有引物组合Ｅ－ＡＧＣ／Ｍ－ＣＡＡ在基因池 间表现多态性，用双亲、Ｆ_１、Ｆ_２单株以及生产和育种上的骨干不育系与恢复系验证均表明这组 引物所揭示的多态性片段与恢复基因有关（命名为ＡＰ_１）。ＡＰ_１为单拷贝，与恢复基因间的距离 为 ４．７６ｃＭ。

黄瓜种质资源遗传多样性及其亲缘关系的AFLP分析

采用AFLP分子标记技术 ,对中国黄瓜种质资源遗传多样性及其与外来种质的关系进行了分析 ,结果表明 8对AFLP引物在 70份黄瓜种质中共扩增出 4 2 5条带 ,多态性带的比例为 6 6 %。供试黄瓜种质的平均期望杂合度为 0 376 ,中国种质的平均期望杂合度为 0 387,明显高于国外种质的 0 2 91。西双版纳黄瓜和印度野生黄瓜具有一些栽培种质没有的特异位点 ,中国栽培种质的特异位点多于外来栽培种质 ,后者也有一些中国栽培种质没有的特异位点。聚类分析将 70份种质分为三大组群 ,即西双版纳黄瓜 (CucumissativusL .var.xishuangbannanesisQietYuan)组群 ,C .sativusvar.hardwickii野生黄瓜组群和栽培黄瓜组群。西双版纳黄瓜与栽培黄瓜的距离最远 ,与野生黄瓜次之。按一定的遗传距离可以将中国和外来栽培种质分开。大多数华南型和华北型种质归属于不同的亚组。

花生黄曲霉侵染抗性的AFLP标记

本研究利用抗、感黄曲霉侵染的花生品种为亲本配制杂交组合“中花5号×J11”,以其F2分离群体为研究材料,采用AFLP技术和BSA分析方法,获得了与花生黄曲霉菌侵染抗性连锁的2个分子标记,标记与抗性间的遗传距离分别为8.8 cM和6.6 cM;利用获得的分子标记对抗、感黄曲霉的花生种质资源进行了分子鉴定,试验结果表明,分子标记与抗性鉴定结果具有较高的一致性,证实了两标记应用于研究群体之外的育种潜力。该抗侵染分子标记的建立为开展花生抗黄曲霉侵染辅助选择育种提供了有效的筛选技术。