Evaluation of Genetic Diversity of Sichuan Common Wheat Landraces in China by SSR Markers

Genetic diversity of 62 Sichuan wheat landraces accessions of China was investigated by agronomic traits and SSR markers. The landrace population showed the characters of higher tiller capability and more kernels/spike, especially tiller no./plant of six accessions was over 40 and kernels/spike of three accessions was more than 70. A total of 547 alleles in 124 polymorphic loci were detected with an average of 4.76 alleles per locus by 114 SSR markers. Parameters analysis indicated that the genetic diversity ranked as genome A 〉 genome B 〉 genome D, and the homoeologous groups ranked as 5〉4〉3〉1〉2〉7〉6 based on genetic richness （Ri）. Furthermore, chromosomes 2A, 1B and 3D had more diversity than that of chromosomes 4A, 7A and 6B. The variation of SSR loci on chromosomes 1B, 2A, 2D, 3B, and 4B implied that, in the past, different selective pressures might have acted on different chromosome regions of these landraces. Our results suggested that Sichuan common wheat landraces is a useful genetic resource for genetic research and wheat improvement.

Microsatellite Marker Based Assessment of Genetic Diversity among Cultivars, Landraces and Wild Relatives in Rice

India being the primary center of origin for rice had a very large treasure of local land races, most of which are out of cultivation today. The exact genetic potential and their differences from commercial varieties and

Core collection construction of tea plant germplasm in Anhui Province based on genetic diversity analysis using simple sequence repeat markers

The tea plant[Camellia sinensis(L.)O.Kuntze]is an industrial crop in China.The Anhui Province has a long history of tea cultivation and has a large resource of tea germplasm with abundant genetic diversity.To reduce the cost of conservation and utilization of germplasm resources,a core collection needs to be constructed.To this end,573 representative tea accessions were collected from six major tea-producing areas in Anhui Province.Based on 60 pairs of simple sequence repeat(SSR)markers,phylogenetic relationships,population structure and principal coordinate analysis(PCoA)were conducted.Phylogenetic analysis indicated that the 573 tea individuals clustered into five groups were related to geographical location and were consistent with the results of the PCoA.Finally,we constructed a core collection consisting of 115 tea individuals,accounting for 20%of the whole collection.The 115 core collections were considered to have a 90.9%retention rate for the observed number of alleles(Na),and Shannon’s information index(I)of the core and whole collections were highly consistent.Of these,39 individuals were preserved in the Huangshan area,accounting for 33.9%of the core collection,while only 10 individuals were reserved in the Jinzhai County,accounting for 8.9%of the core set.PCoA of the accessions in the tea plant core collection exhibited a pattern nearly identical to that of the accessions in the entire collection,further supporting the broad representation of the core germplasm in Anhui Province.The results demonstrated that the core collection could represent the genetic diversity of the original collection.Our present work is valuable for the high-efficiency conservation and utilization of tea plant germplasms in Anhui Province.

Genetic Diversity of Maize Populations Developed by Two Kinds of Recurrent Selection Methods Investigated with SSR Markers

Two cycles of biparental mass selection （MS） and one cycle of half-sib-S3 family combining selection （HS-S3） for yield were carried out in 2 synthetic maize populations P4C0 and P5C0 synchronously. The genetic diversity of 8 maize populations, including both the basic populations and their developed populations, were evaluated by 30 SSR primers. On the 30 SSR loci, a total of 184 alleles had been detected in these populations. At each locus, the number of alleles varied from 2 to 14, with an average of 6.13. The number and ratio of polymorphic loci in both the basic populations were higher than those of their developed populations, respectively. There was nearly no difference after MS but decreased after HS-S3 in both the basic populations in the mean gene heterozygosity. The mean genetic distance changed slightly after MS but decreased in a bigger degree after HS-S3 in both the basic populations. Analyses on the distribution of genetic distances showed that the ranges of the genetic distance were wider after MS and most of the genetic distances in populations developed by HS-S3 were smaller than those in both the basic populations. The number of genotypes increased after MS but decreased after HS-S3 in both the basic populations. The genetic diversity of intra-population was much more than genetic diversity of inter-population in both the basic populations. All these indexes demonstrated that the genetic diversity of populations after MS was similar to their basic populations, and the genetic diversity was maintained during MS, whereas the genetic diversity of populations decreased after HS-S3. This result indicated that heterogeneity between some of the individuals in the developed populations increased after MS, whereas the populations become more homozygotic after HS-S3.

SSR markers development and their application in genetic diversity evaluation of garlic(Allium sativum)germplasm

Garlic(Allium sativum),an asexually propagated vegetable and medicinal crop,has abundant genetic variation.Genetic diversity evaluation based on molecular markers has apparent advantages since their genomic abundance,environment insensitivity,and non-tissue specific features.However,the limited number of available DNA markers,especially SSR markers,are insufficient to conduct related genetic diversity assessment studies in garlic.In this study,4372 EST-SSR markers were newly developed,and 12 polymorphic markers together with other 17 garlic SSR markers were used to assess the genetic diversity and population structure of 127 garlic accessions.The averaged polymorphism information content(PIC)of these 29 SSR markers was 0.36,ranging from 0.22 to 0.49.Seventy-nine polymorphic loci were detected among these accessions,with an average of 3.48 polymorphic loci per SSR.Both the clustering analyses based on either the genotype data of SSR markers or the phenotypic data of morphological traits obtained genetic distance divided the 127 garlic accessions into three clusters.Moreover,the Mantel test showed that genetic distance had no significant correlations with geographic distance,and weak correlations were found between genetic distance and the phenotypic traits.AMOVA analysis showed that the main genetic variation of this garlic germplasm collection existed in the within-population or cluster.Results of this study will be of great value for the genetic/breeding studies in garlic and enhance the utilization of these garlic germplasms.

Genetic Diversity Assessment of Acid Lime (<i>Citrus aurantifolia</i>Swingle) Landraces in Nepal, Using SSR Markers

Acid lime (Citrus aurantifolia) is an important commercial fruits crop, cultivated in terai to high hills of Nepal. High variation of acid lime fruits are observed in existing landraces due to crossing within the other citrus species. Determination of genetic variation is important to the plant breeders for development of high yielding variety and hybrids. Therefore, an attempt has been made to study the genetic diversity of 62 acid lime landraces, collected from different altitudinal range in the eastern part of Nepal, using SSR markers. Twelve Simple Sequence Repeat (SSR) primer pairs were used to assess the genetic diversity of acid lime. The average genetic similarity level among the 62 accessions was 0.77, ranging from 0.54 to 1.0 and separated five major cluster groups. Total of 33 alleles were detected by eleven primer pairs and size of alleles ranged from 50 to 225. Average polymorphic information content (PIC) value was 0.50, whereas highest 0.75 and lowest 0.18 was observed in CAT01 and GT03 loci respectively. The results of the study clearly indicated that, SSR markers are highly polymorphic and more informative for the assessment of genetic diversity of acid lime landraces.

SSR Analysis of Genetic Diversity Among 192 Diploid Potato Cultivars

In potato breeding,it is difficult to improve the traits of interest at the tetraploid level due to the tetrasomic inheritance.A promising alternative is diploid breeding.Thus it is necessary to assess the genetic diversity of diploid potato germplasm for efficient exploration and deployment of desirable traits.In this study,we used SSR markers to evaluate the genetic diversity of diploid potato cultivars.To screen polymorphic SSR markers,55 pairs of SSR primers were employed to amplify 39 cultivars with relatively distant genetic relationships.Among them,12 SSR markers with high polymorphism located at 12 chromosomes were chosen to evaluate the genetic diversity of 192 diploid potato cultivars.The primers produced 6 to 18 bands with an average of 8.2 bands per primer.In total,98 bands were amplified from 192 cultivars,and 97 of them were polymorphic.Cluster analysis using UPGMA showed the genetic relationships of all accessions tested:186 of the 192 accessions could be distinguished by only 12 pairs of SSR primers,and the 192 diploid cultivars were divided into 11 groups,and 83.3% constituted the first group.Clustering results showed relatively low genetic diversity among 192 diploid cultivars,with closer relationship at the molecular level.The results can provide molecular basis for diploid potato breeding.

Research Progress of Molecular Markers in Genetic Diversity of Rapeseed

In recent years,with the continuous improvement and development of molecular technology in the application process,different types of DNA molecular markers have made rapid progress in the study of genetic diversity of rapeseed. The study of genetic diversity is conducive to the correct formulation of the strategy of collecting and in situ preservation of genetic resources of rapeseed,and it is the genetic basis for the improvement of rapeseed varieties. This article mainly starts with the three DNA molecular markers( SSR,RAPD,AFLP) widely used in the study of genetic diversity of rapeseed. By introducing the application principles and characteristics of SSR,RFPD and AFLP molecular markers,research progress of these three marker technologies in genetic diversity of rapeseed is briefly described.

Assessment of Genetic Diversity of NIFOR Oil Palm Main Breeding Parent Genotypes Using Microsatellite Markers

The genetic diversity among 15 NIFOR breeding parents was assessed using 10 microsatellite markers. A high genetic diversity was observed with a total of 64 alleles including 23 rare alleles or alleles at frequencies less than 0.05. The NIFOR tenera parents recorded the highest number of rare alleles. The average observed heterozygosity and mean gene diversity across all parental groups were 0.6889 and 0.7029, respectively. Higher genetic diversity was detected among the NIFOR dura and tenera parents compared to that of the Deli dura parents in absolute terms. Analysis of molecular variance (AMOVA) showed that 87% of the total variation (p < 0.001) observed was due to differences among parents. Rogers’ genetic distance ranged from 0.2988 to 0.8000 (mean = 0.5570). The dendrogram constructed on the basis of Rogers’ genetic distance clustered the parents in three groups. They generally clustered in heterotic manner rather than by geographic origins. The groupings obtained through PCoA confirmed the results obtained by cluster analysis. The results obtained are strong assets for NIFOR breeding programme.

Genetic Relationships between Cultivated and Wild Olive Trees (Olea Europaea L. Var. Europaea and Var. Sylvestris) Based on Nuclear and Chloroplast SSR Markers

The olive is widely cropped in Tunisia where also oleaster trees thrive all around orchards and in natural sites. Little is known on the genetic relationships between the olive crop and oleaster trees in Tunisia. Fifty-two oleaster trees and fifteen cultivars were sampled from Tunisia. SSR genotyping was performed in polyacrylamide gels after fluorescent labeling. We used seven nuclear and two chloroplast SSR markers. AFC analyses showed close genetic relationships between cultivated and oleaster trees. Genetic relationships were also displayed in a dendrogram based on Unweighted Pair Group Method (UPGMA). Five clusters were defined mixing cultivar and oleaster trees suggesting close relationship between some cultivar and some oleaster trees. One oleaster is single in a cluster. The chlorotype SSR markers show probably three olive origins. Some cultivars have the CE chlorotype originates from the East of the Mediterranean basin, the CCK haplotype originates from Maghreb and the COM chlorotype originates from West Mediterranean. The cultivars were 1) introduced from the East;2) selected in the West;3) or selected in the North Africa region. The Tunisian oleaster trees carry eastern and western Mediterranean chlorotype CCK, COM and CE.

Assessment of genetic diversity in broomcorn millet (Panicum miliaceum L.) using SSR markers

The genetic diversity of 118 accessions of broomcom millet （Panicum miliaceum L.）, collected from various ecological areas, was analyzed. Using 46 SSR （Simple Sequence Repeat） polymorphic markers from rice, wheat, oat and barley, a total of 226 alleles were found, which exhibited moderate level of diversity. The number of alleles per primer ranged from two to nine, with an average of 4.91. The range of polymorphism information content （PIC） was 0.2844）.980 （average, 0.793）. The expected heterozygosity （He） varied from 0.346 to 0.989, with an average of 0.834. The average coefficient of the genetic similarity of SSR markers among the 118 accessions was 0.609, and it ranged from 0.461 to 0.851. The UPGMA （Unweight Pair Group Method with Arithmetic Mean） clustering analysis at the genetic similarity value of 0.609 grouped the 118 accessions into five groups. Mantel test meant that geographical origin and genetic distance presented positive correlation. The clustering results were consistent with known information on ecological growing areas. The genetic similarity coefficient of the accessions in the Loess Plateau ecotype was significantly lower than those in the other ecotypes. It indicates that the highest level of genetic diversity occurred in the Loess Plateau, which is probably the original site of Panicum miliaceum.

A Comparative Analysis of B Chromosomes and Genetic Diversity in Maize (Zea mays L.) Landraces from Southwest China

The number of B chromosomes （Bs） in 54 maize landraces from Southwest China was tested by means of cytological observations. Nine landraces with Bs were observed. A map, showing the geographic distribution of the landraces with Bs, was plotted. It was found that southeastern Sichuan Province in China was the main distribution area of the landraces with Bs in Southwest China. In order to obtain information on relationships between Bs and genetic variation, genetic diversity both among and within 11 landraces was evaluated. For each SSR marker, the number of alleles ranged from 3 to 12 with an average of 7.86, which revealed a high level of genetic diversity among maize landraces in Southwest China. Based on SSRs data, higher genetic variation was found in the landraces with 2B, and the genetic distance between the landraces with and without Bs was higher. The results together with the principal component analysis （PCA） supported the hypothesis that maize landraces in Southwest China were first introduced to the middle part of southwest Sichuan, China. At the same time, the effect of Bs on genetic variation was discussed.

Mating system and progeny genetic diversity of Camellia oleifera ‘Ruan Zhi’

Camellia oleifera Abel.is an important economic tree species of southern China.In this study,we evaluated the mating system and genetic diversity of a series of cultivars of C.oleifera‘Ruan Zhi’.A total of 159 individuals from the progenies of four cultivars were tested by simple sequence repeat molecular markers.Results reveal that 11 pairs of primers showed polymorphism and their polymorphism information content value was greater than 0.73,suggesting that these primers could be used to identify the genetic diversity of open-pollinated populations.The average number of effective alleles(Ne=4.88)was significantly different from the average number of alleles(Na=12.18),and their distribution in the sample population was not uniform.The average observed heterozygosity(Ho=0.96)was greater than the average expected heterozygosity(He=0.79),and the population heterozygote was excessive.Shannon index was 1.84 and populations showed high genetic diversity.As regards to the mating system,the multilocus outcrossing rate was 0.996,and the single locus 0.866.These results indicate a high degree of outcrossing by C.oleifera‘Ruan Zhi’.We recommend selecting individuals for high genetic gain from the progenies of cultivars because of outcrossing characteristics and genetic diversity for application to germplasm conservation and promotion.

Genetic diversity of Chinese summer soybean germplasm revealed by SSR markers

There are abundant soybean germplasm in China. In order to assess genetic diversity of Chinese sum- mer soybean germplasm, 158 Chinese summer soybean ac- cessions from the primary core collection of G. max were used to analyze genetic variation at 67 SSR loci. A total of 460 alleles were detected, in which 414 and 419 alleles oc- curred in the 80 Huanghuai and the 78 Southern summer accessions, respectively. The average number of alleles per locus was 6.9 for all the summer accessions, and 6.2 for both Huanghuai and Southern summer accessions. Marker diver- sity (D) per locus ranged from 0.414 to 0.905 with an average of 0.735 for all the summer accessions, from 0.387 to 0.886 with an average of 0.708 for the Huanghuai summer acces- sions, and from 0.189 to 0.884 with an average of 0.687 for the Southern summer accessions. The Huanghuai and Southern summer germplasm were different in the specific alleles, allelic-frequencies and pairwise genetic similarities. UPGMA cluster analysis based on the similarity data clearly separated the Huanghuai from Southern summer soybean accessions, suggesting that they were different gene pools. The results indicate that Chinese Huanghuai and Southern summer soybean germplasm can be used to enlarge genetic basis for developing elite summer soybean cultivars by ex- changing their germplasm.

Genetic Diversity Analysis of 13 Maize Inbred Lines by SSR Molecular Markers

This paper used SSR molecular markers to perform the genetic diversity analysis on 13 ordinary inbred lines of maize of different sources in order to divide heterotic groups of maize inbred line and predict heterosis. Using 12 pairs of SSR primers,a total of 47 allelic variants were detected in 13 inbred lines,2-5 alleles were detected for each pair of primers,an average of 3. 9,and polymorphism information content varied from 0. 379 to 0. 828. According to the cluster analysis,the 13 inbred lines could be divided into 5 groups.

珍稀濒危植物石山苏铁的SSR引物设计和遗传多样性分析

揭示珍稀濒危植物石山苏铁(Cycas sexseminifera)种群的遗传多样性水平和遗传分化大小,确定优先保护种群,对石山苏铁的有效保护和管理策略的制定具有重要意义。本研究基于简化基因组序列分析设计Simple Sequence Repeats(SSR)引物,并利用SSR引物进行遗传多样性检测。实验共获得6对SSR引物,6对引物共检测出37个观测等位基因(N a),其中最小观测等位基因数目为3,最大观测等位基因数目为12,平均每个位点等位基因数目为6.167。位点GZST002、GZST055、GZST065、GZST088是高度多态性位点(PIC>0.5)。石山苏铁各种群期望杂合度(H e)为0.330-0.533,平均值为0.444,表明石山苏铁遗传多样性处于中等水平;7个种群的H e值大小顺序为广西植物研究所引种(ZWS)>崇左广河(GH)>崇左排汝(PR)>隆安陇怀(LH)>崇左中干(ZG)>百色作登(ZD)>隆安新会(XH)。固定系数(F)为-0.161-0.480,平均值为0.074,其中LH、PR、XH 3个野生种群为负值,GH、ZD、ZG 3个野生种群的固定系数则大于0;7个种群的F值大小顺序为百色作登(ZD)>广西植物研究所引种(ZWS)>崇左中干(ZG)>崇左广河(GH)>隆安陇怀(LH)>隆安新会(XH)>崇左排汝(PR)。因此,综合各个遗传指标,石山苏铁需要重点保护和引种的野生种群是遗传多样性相对较高的崇左广河(GH)种群。同时建议开发更多的SSR引物和采集更广范围的石山苏铁野生种群,精准筛选遗传多样性高的优良种群,以利于更全面和准确地评估石山苏铁的遗传多样性水平和濒危机制。

基于种实表型性状和SSR标记的杉木2代种子园遗传多样性分析

【目的】从表型和分子2个角度评估江西信丰县国家杉木良种基地杉木2代种子园的遗传多样性,明确种子园的遗传背景,为后期种子园的改良(去劣疏伐)、重建(亲本选择与配置)等提供依据,同时为开展杂交育种提供遗传信息。【方法】以江西信丰杉木2代种子园内51个建园无性系为研究对象,通过分析8个种实表型性状掌握种子园不同无性系间种实性状的差异,同时利用SSR标记从DNA水平进行遗传多样性评估。【结果】供试51个无性系在种实表型性状和DNA水平上均存在明显的变异和较丰富的遗传多样性。8个表型性状变异系数为10.53%~37.04%,其中球果和种子的平均变异系数分别为18.99%和14.01%,种子的变异系数较小,表明种子的稳定性要比球果的高;种实性状的Shannon-Weaver多样性信息指数平均为2.060,表明种实性状的多样性较丰富。在DNA水平,14个SSR标记在51个无性系中共扩增出68个等位位点,平均Shannon’s信息指数、平均Nei’s遗传多样性指数、平均观测杂合度和平均期望杂合度分别为0.925、0.506、0.486和0.511,表明信丰杉木2代种子园遗传多样性较丰富。基于种实表型性状和SSR标记均可将51个无性系分为两大类群,但两者的具体聚类结果存在较大差异,Mantel检验显示种实性状与SSR标记之间不存在相关性(r=0.064,P=0.870>0.05)。【结论】信丰杉木2代种子园遗传多样性较丰富,具有再选择空间和改良潜力。

Assessment of genetic variation in tomato (Solanum lycopersicum L.) inbred lines using SSR molecular markers

A study was conducted to determine the genetic diversity of 39 determinate and indeterminate tomato inbred lines collected from China, Japan, S. Korea, and USA. Using 35 SSR polymorphic markers, a total of 150 alleles were found with moderate levels of diversity, and a high number of unique alleles existing in these tomato lines. The mean number of alleles per locus was 4.3 and the average polymorphism information content （PIC） was 0.31. Unweighted Pair Group Method with Arithmetic Mean （UPGMA） clustering at genetic similarity value of 0.85 grouped the inbred lines into four groups, where one USA cultivar formed a separate and more distant cluster. The most similar inbred lines are from USA, both with determinate type, whereas the most different lines are from USA （Us-16） and Japan （Ja-2） with determinate and indeterminate growth habit, respectively. Clustering was consistent with the known information regarding geographical location and growth habit. The genetic distance information reported in this study might be used by breeders when planning future crosses among these inbred lines.

Genetic diversity analysis of Sinojackia microcarpa, a rare tree species endemic in China, based on simple sequence repeat markers

Although most Sinojackia species are endangered, they contribute greatly to the biodiversity of local ecosystems. Sinojackia microcarpa, an endangered species, is distributed only in three provinces of eastern China. Determining the genetic diversity of S. microcarpa provides key information for germplasm evaluation and species conservation. Here we used simple sequence repeat (SSR) markers to investigate the genetic diversity of eight natural populations of S. microcarpa. Leaf samples were collected from 144 individuals in 8 wild populations. The 156 bands were generated from 14 pairs of informative SSR primers, with an average percentage of polymorphic bands of 45.67%. The average values of Nei’s genetic diversity (He) and Shannon’s diversity index (I) were 0.1007 and 0.1658, respectively. The total genetic variation of S. microcarpa existed mainly within the eight populations, rather than among populations, and reached 86.41%. A cluster analysis showed that the eight wild populations of S. microcarpa could be classified into four groups, at a threshold of 4.0, based on an analysis of the SSR genotypes. Furthermore, there was a significant association between the phylogenetic relationships and the geographic locations of the S. microcarpa populations. In particular, populations from Fuyang, Jiande, and Lin’an in Zhejiang Province had close phylogenetic relationships and geographic distances. In addition, these three populations had the highest genetic diversity and the most individuals, suggesting that these three locations may be the S.microcarpa distribution center. This study serves as a model for studying the genetic diversity of endangered plant species.

THE GENETIC DIVERSITY OF GAOZHOU WILD RICE ANALYZED BY SSR

The genetic diversity of total 240 acces- sions of common wild rice coming from Gaozhou, Shaoguan, Zhanjiang, and other places in Guang- dong, and Jiangxi, Fujian, Yunnan provinces, etc. in China and South-eastern Asia was evaluated by us- ing 24 pairs of SSR primers. The results indicated that: (i) there were 17 polymorphic loci in 24 pairs of SSR primers, and the average percentage of poly- morphic loci was 69%; the average total number of alleles, the average number of alleles per locus and the average number of alleles per polymorphic loci were 51.1, 2.04 and 2.43, respectively; (ii) the aver- age gene diversity was 0.8447. There were remark- able differentiations among 5 populations of Gaozhou wild rice. All the above-mentioned genetic parame- ters indicated that Gaozhou wild rice of Pengshan Village (or Bei Toudong) of Zhenjiang Town should be a center of genetic differentiation and diversity of Gaozhou wild rice. Gaozhou wild rice is probably the largest center of genetic differentiation and diversity of common wild rice from Guangdong Province, South China and even the whole China.