Microsatellite markers for the common bean Phaseolus vulgaris

Efforts to develop molecular tools for genetic analysis and breeding of common bean in the tropics are still limited. The number of microsatellite markers available for the crop is small compared to other crops of similar social and economic importance. As part of a project to broaden the use of molecular tools in bean breeding, a genomic library enriched for AG/TC repeat sequences was constructed for Phaseolus vulgaris. Twenty microsatellite markers were initially developed and 10 were characterized using a panel of 85 representative accessions of the bean gene bank. The number of alleles per marker ranged from three to 10. The polymorphism information content (PIC) varied from 0.23 to 0.80. The results indicate that the new markers can be readily used in genetically analysis of common bean.     

Isolation and characterization of eight compound microsatellite markers in a mangrove tree Kandelia candel (L.) Druce

Kandelia candel is an important mangrove tree species of family Rhizophoraceae. Here we isolated eight codominant compound microsatellite simple sequence repeat (SSR) loci from K. candel. Our isolated loci provided compound SSR markers with polymorphism of three to 11 alleles per locus. The expected and observed heterozygosities ranged from 0.230 to 0.887 and from 0.083 to 1.00, respectively. These markers would be the useful tools for analysing questions concerning population genetic structure and mating system of K. candel.     

Use of molecular markers in participatory plant breeding: assessing the genetic variability in cotton populations bred by farmers

In participatory plant breeding, farmers are involved in simple selection schemes that are not suitable for assessing genetic variability in the segregating populations. We propose to use information derived from molecular marker analyses to help monitoring such populations. In this study, we used three indicators to compare genetic variability in eight genetic structures, that is three plant populations selected by farmers over five generations, three nonselected populations and two commercial varieties. The three indicators were the polymorphic locus rate, heterozygosity rate and dissimilarity index. The results highlighted that the genetic variability decreased more with farmers’ selection than with environmental factors. The breeding process was not complete because genetic variability in the selected populations was midway between that of the nonselected populations and that of the commercial varieties monitored. The three proposed indicators were relevant for describing the studied populations. They could be interpreted according to a grid drawn up on the basis of the results of the present study.     

Development of microsatellite markers and characterization of simple sequence length polymorphism (SSLP) in rice (Oryza sativa L.)

Microsatellite markers containing simple sequence repeats (SSR) are a valuable tool for genetic analysis. Our objective is to augment the existing RFLP map of rice with simple sequence length polymorphisms (SSLP). In this study, we describe 20 new microsatellite markers that have been assigned to positions along the rice chromosomes, characterized for their allelic diversity in cultivated and wild rice, and tested for amplification in distantly related species. Our results indicate that the genomic distribution of microsatellites in rice appears to be random, with no obvious bias for, or clustering in particular regions, that mapping results are identical in intersubspecific and interspecific populations, and that amplification in wild relatives ofOryza sativa is reliable in species most closely related to cultivated rice but becomes less successful as the genetic distance increases. Sequence analysis of SSLP alleles in three relatedindica varieties demonstrated the clustering of complex arrays of SSR motifs in a single 300-bp region with independent variation in each. Two microsatellite markers amplified multiple loci that were mapped onto independent rice chromosomes, suggesting the presence of duplicated regions within the rice genome. The availability of increasing numbers of mapped SSLP markers can be expected to increase the power and resolution of genome analysis in rice.     

PCR analysis of oilseed rape cultivars (Brassica napus L. ssp. oleifera) using 5′ -anchored simple sequence repeat (SSR) primers

Primers complementary to simple sequence repeats (SSRs) and with variable three-base anchors at their 5 end, were used in PCR analyses to compare pooled DNA samples from various Brassica napus and B. rapa cultivars. Amplification products were resolved on polyacrylamide gels and detected by silver-nitrate staining. The resulting banding patterns were highly repeatable between replicate PCRs. Two of the primers produced polymorphisms at 33 and 23 band positions, respectively, and could each discriminate 16 of the 20 cultivars studied. Combined use of both primers allowed all 20 cultivars to be distinguished. The UPGMA dendrogram, based on the cultivar banding profiles, demonstrated clustering on the basis of winter/spring growth habit, high/low glucosinolate content, and cultivar origin (i.e. the breeder involved). Intracultivar polymorphism was investigated using a minimum of ten individuals for each cultivar and was found to vary considerably between cultivars. It is concluded that anchored SSR-PCR analysis is a highly informative and reproducible method for fingerprinting oilseed rape populations, but that intra-cultivar variation should be investigated before using banding profiles from pooled samples for the identification of individuals.     

The medical utility of genomics data in neuropsychiatry: mutational genetics versus association genetics

The long anticipated ‘genetic revolution’ in neuropsychiatry has yet to have an impact on the practice of clinical medicine. Excitement in the 1980s over major genetic breakthroughs in schizophrenia and manic depression, for example, has been replaced in the late 1990s by the sobering realization that most common neuropsychiatric disorders are multifactorial. Despite considerable effort and resources, no ‘causative’ genetic variation has been identified that plays a definitive major role in any common neuropsychiatric disorder.     

黑河上游灌丛建群种中国沙棘自由授粉子代父本分析和花粉流

利用SSR分子标记对中国沙棘（Hippophae rhamnoides ssp. sinensis Rousi）自由授粉的种子进行父本分析,研究其子代的父本来源和花粉散布模式。结果显示：在80%的置信水平上,193个子代中有104个个体可以确定花粉来源;在20个确定的父本中,16个为中国沙棘,4个为肋果沙棘（H.neurocarpa S.W.Liu et T.N.He）。传粉格局分析结果显示,中国沙棘有效花粉散布范围为3~71 m,平均距离为20.4 m,2株母本分别有87.23%和78.95%的有效花粉来自距其30 m的范围之内,研究结果表明中国沙棘自然种群以近距离传粉为主。此外,在黑河上游沙棘杂交带中,中国沙棘子代中的肋果沙棘花粉平均贡献率达到14.84%,表明中国沙棘与肋果沙棘存在较高的种间当代花粉流。     

Genetic diversity of Puccinia kuehnii,the causal agent of orange rust of sugarcane,from Brazil

The use of resistant genotypes is the preferred method to control orange rust of sugarcane (Saccharum spp) caused by Puccinia kuehnii. This approach has been adopted in Brazil but outbreaks of the disease on previously resistant varieties showed that the efficacy of this method is limited and requires a better understanding of pathogen diversity. Nevertheless, adequate molecular markers for examining pathogen diversity at population level are not available, which limits the success of orange rust control by genetic resistance. Therefore, two independent investigations were conducted to examine genetic diversity of P. kuehnii from São Paulo state, the most important sugarcane growing state of Brazil. First, simple-sequence repeat (SSR) markers were developed in the present work and genotypic diversity of orange rust isolates from different locations investigated. Second, phenotypic diversity was examined by the single-pustule inoculation technique on P. kuehnii isolates retrieved from three susceptible commercial sugarcane cultivars. A total of 96 SSR markers were generated and tested for this species. Subsequently, 29 isolates of P. kuehnii were fingerprinted with nine SSR markers to estimate the genotypic diversity by neighbour-joining and 3D principal coordinates. The 29 isolates of the pathogen clustered into four main groups, which were identified by three SSR markers (NPRL_PK_108a, NPRL_PK_162_spka and NPRL_PK_221_spka). Phenotypic data at 21 days after the single-pustule inoculation showed that P. kuehnii from highly susceptible commercial cultivars harboured a small proportion of variants capable of causing disease on resistant cultivars. A differential reaction was demonstrated for the most virulent variant in a repeated experiment confirming the existence of races within P. kuehnii in Brazil.     

Studies on reproductive strategies of Vitex negundo L. var. heterophylla (Franch.) Rehder (Lamiaceae) based on morphological characteristics and SSR markers

Vitex negundo L. var. heterophylla (Franch.) Rehder (Lamiaceae) is an important tree species for soil and water conservation, yet the reproductive ecology of this species remains to be elucidated. To investigate the reproductive traits of V. negundo var. heterophylla, the phenology, morphological characteristics (a suite of characters was assessed: floral morphology, nectar production, pollen viability, and stigma receptivity) and mating system of this species were systematically revealed for the first time in this study. Phenological observations, morphological measurements, and nectar production analysis were conducted during anthesis. Pollen viability and stigma receptivity at different flowering stages were measured by biochemical methods. Finally, genetic analysis based on SSR markers was used to reveal the mating system; outcrossing index and pollen‐ovule ratio were also calculated to help analysis. V. negundo var. heterophylla showed several obvious characteristics of outcrossing, such as abundant and attractive flowers, secreting nectar, and emitting scent. In addition, mechanisms such as homogamy and a short anther‐stigma distance that can promote self‐fertilization were also identified in this species. The coexistence of selfing and outcrossing characteristics demonstrates a predominantly outcrossed mixed mating system (outcrossing rate, t = 95%). The scientific information provided by this study may contribute to conservation of V. negundo var. heterophylla from a reproductive perspective.     

Assessment of genetic diversity and phylogenetic relationship among grouper species Epinephelus spp. from the Saudi waters of the Arabian Gulf

Understanding of fish genetic characterization plays a vital role in the conservation and utilization of fish genetic resources of grouper species. The present study was carried out to assess the genetic diversity and phylogenetic relationships in five grouper species, Epinephelus spp. from eastern Saudi Arabian coast using two molecular marker systems, inter simple sequence repeat (ISSR) and microsatellite (SSR) markers. In total, 219 individuals grouper specimens (Epinephelus tauvina, E. coioides, E. bleekeri, E. malabaricus, and E. areolatus) were genotyped with 10 ISSR and 11 SSR selected primers. The ISSR produced 94 DNA fragments, of which 44 were polymorphic with an average of 2.13 fragment per primer. While SSR primers generated 107 alleles, all of them were polymorphic with an average 9.72 per primer. ISSR and SSR techniques demonstrated a high level of gene diversity and genetic distances illustrated by UPGMA dendrograms among the grouper species. The results proved that the SSR markers were highly informative and efficient in detecting genetic variability and relationships of the Epinephelus spp.