Description and analysis of genetic diversity between commercial bean lines (Phaseolus vulgaris L.)

The effectiveness of RFLP, DAMD-PCR, ISSR and RAPD markers in assessing polymorphism and relationships between 24 commercial lines of Phaseolus vulgaris L.was evaluated. We have used a Phaseolus-specific minisatellite sequence as a probe, which enabled 23 of the bean lines tested to be fingerprinted. Based on the sequence information obtained, primers corresponding to the bean-specific minisatellite core sequence were used in subsequent PCR amplifications. Our observations indicated that while the DAMD-PCR was sensitive in detecting genetic variation between bean species and between accessions of P. vulgaris, when used alone it may be limited in its ability to detect genetic variation among cultivated bean lines due to the low number of loci amplified. Only one out of the five ISSR primers tested was efficient in generating multiple band profiles, which was insufficient to distinguish all the different bean lines. Reproducible RAPD profiles were obtained, and these allowed us to differentiate all the genotypes tested with seven primers. We ultimately used only results from RFLP and RAPD markers to explore the genetic diversity among commercial bean lines. Both analyses led to the same clustering of the bean lines according to their geographical origins (United States or Europe). With respect to the European lines, the results obtained from RAPD data also enable the lines to be clustered according to their creators. Received: 15 January 2000 / Accepted: 21 March 2000     

DNA restriction fragment length polymorphisms correlate with isozyme diversity in Phaseolus vulgaris L.

Summary Genetic variation in Phaseolus vulgaris L. (P. vulgaris) was investigated at the isozyme and DNA levels. We constructed a library of size-selected Pst I clones of P. vulgaris nuclear DNA. Clones from this library were used to examine 14 P. vulgaris accessions for restriction fragment length polymorphisms (RFLPs). DNAs from each accession were analyzed with three restriction enzymes and 18 single copy probes. The same accessions were also examined for variability at 16 isozyme loci. Accessions included four representatives of the T phaseolin group and five representatives each of the C and S phaseolin groups. One member of the S group (the breeding line XR-235-1-1) was derived from a cross between P. vulgaris and P. coccineus. Isozymes and RFLPs revealed very similar patterns of genetic variation. Little variation was observed among accessions with C and T phaseolin types or among those with the S phaseolin type. However, both isozyme and RFLP data grouped accessions with S phaseolin separately from those accessions with C or T phaseolin. The highest degree of polymorphism was observed between XR-235-1-1 and members of the C/T group. RFLP markers will supplement isozymes, increasing the number of polymorphic loci that can be analyzed in breeding, genetic, and evolutionary studies of Phaseolus.     

Mitochondrial restriction fragment length polymorphisms in wild Phaseolus vulgaris L.: insights on the domestication of the common bean

Summary Previous examination of intraspecific mitochondrial DNA (mtDNA) diversity in common bean, Phaseolus vulgaris, showed that five restriction fragment length polymorphisms (RFLPs) distinguish the mitochondrial genomes of the two major gene pools of cultivated beans, the Mesoamerican and the Andean. In the study presented here, mtDNA was used to compare the amount of diversity in cultivated beans to that in collections of wild beans to gain an understanding of how and when the mitochondrial genomes of the gene pools became distinct. The mtDNA of six wild bean accessions from Central and South America were digested with nine restriction endonucleases and analyzed by Southern hybridization. A total of twenty RFLPs were detected demonstrating a significantly higher amount of mtDNA variability in wild beans than in cultivated ones. All of the wild beans had the same mtDNA pattern for four out of the five inter-gene pool RFLPs, indicating that the polymorphism arose soon after domestication: two in the gene pool of the cultivated Mesoamerican beans and two in the gene pool of the cultivated Andean beans. The fifth RFLP must have occurred before domestication since the locus was also polymorphic in the wild beans. Wild beans from the south Andes were distinct and less variable than wild accessions of the north Andes and Mesoamerica. The distribution of mtDNA RFLPs among the wild beans supports the concept of two distinct domestication events for P. vulgaris.     

Evolution of genetic diversity during the domestication of common-bean (Phaseolus vulgaris L.)

M13 DNA fingerprinting was used to determine evolutionary changes that occurred in Latin American germ plasm and USA cultivars of commonbean (Phaseolus vulgaris L.) during domestication. Linkage mapping experiments showed that M13-related sequences in the common-bean genome were either located at the distal ends of linkage groups or that they were unlinked to each other or to any previously mapped markers. Levels of polymorphism observed by hybridization with M13 (1 probe-enzyme combination) were comparable to those observed by hybridization with single-copy random PstI genomic probes (36 enzyme-probe combinations) but were higher than those observed for isozymes (10 loci). Results indicated that the wild ancestor had diverged into two taxa, one distributed in Middle America (Mexico, Central America, and Colombia) and the other in the Andes (Peru and Argentina); they also suggested separate domestications in the two areas leading to two cultivated gene pools. Domestication in both areas led to pronounced reductions in diversity in cultivated descendants in Middle America and the Andes. The marked lack of polymorphism within commercial classes of USA cultivars suggests that the dispersal of cultivars from the centers of origin and subsequent breeding of improved cultivars led to high levels of genetic uniformity. To our knowledge, this is the first crop for which this reduction in diversity has been documented with a single type of marker in lineages that span the evolution between wild ancestor and advanced cultivars.     

Genetics of fertility restoration in cytoplasmic male sterile Phaseolus vulgaris L.

Summary Restoration of fertility in cytoplasmic male sterile Phaseolus vulgaris by line R-351 was controlled by a single gene. The restorer gene (Fr) displayed incomplete dominance leading to partial restoration of fertility in F₁ generations; full restoration was not achieved until the F₂ generation. Once full restoration of fertility was produced in the F₂ generation, no segregation for sterility was observed in subsequent generations derived from heterozygotes Frfr, either by testcrossing (restored × maintainer) or in F₃ progenies. Implications of the irreversible nature of this restoration are discussed.Florida Agr. Exp. Sta. Journal Series No. 7733     

Determination of genetic relationships among shape Phaseolus vulgaris populations in a conical cross from RAPD marker analyses

Random-amplified polymorphic DNA (RAPD) markers were used to determine genetic relationships among Phaseolus vulgaris breeding populations. Genetic distances were calculated from the distribution of 317 RAPD markers among 8 parents, 10 individuals from 8 cycle-one populations, 10 individuals from 6 cycle-two populations and 10 individuals from 2 cycle-three populations of a conical cross. Genetic distances between populations and parents were consistent with their degree of relationship in the crossing scheme indicating that a RAPD analysis is a sensitive and useful method for categorizing breeding materials according to their genetic similarities. Genetic variation among individuals within populations increased from cycle one to cycle three and variation among populations within the cycles decreased from cycle one to cycle three in the conical cross. The results showed that this crossing scheme can be used to collect the genetic diversity in eight parents into a single plant breeding population. Abbreviations: CBB, common bacterial blight; GD, genetic distance; RAPD, random-amplified polymorphic DNA     

Large double-stranded RNA molecules in Phaseolus vulgaris L. are not associated with cytoplasmic male sterility

Summary Two large double-stranded RNA molecules, 15 and 16 kilobases, were detected in cytoplasmic male sterile (CMS) Phaseolus vulgaris by agarose gel electrophoresis. A number of smaller RNA molecules were observed in Sprite, a maintainer line, and recurrent backcrossing of CMS P. vulgarisxSprite resulted in a combined electrophoretic pattern of the two large and numerous small RNA molecules. The large RNA molecules were seed and pollen-transmissible, but were not transmitted by grafting. The RNAs were present in revertant and restored lines derived from CMS-Sprite and therefore were not associated with the cytoplasmic male sterile trait.Florida Agr. Exp. Stn. Journal Series No. 8405     

普通菜豆种质资源遗传多样性研究进展

普通菜豆于15世纪从美洲直接引入中国,作为重要的食用豆类作物之一,在我国的许多地区广泛种植。本文对普通菜豆的起源、驯化、传播以及遗传多样性研究等方面的进展进行综述,并根据普通菜豆育种和生产中存在的问题及今后的研究方向提出一些建议,旨在为普通菜豆的种质收集保存以及合理利用提供参考。     

Allozyme variation in domesticated annual sunflower and its wild relatives

 The annual sunflower (Helianthus annuus L.) is a morphologically and genetically variable species composed of wild, weedy, and domesticated forms that are used for ornament, oilseed, and edible seeds. In this study, we evaluated genetic variation in 146 germplasm accessions of wild and domesticated sunflowers using allozyme analysis. Results from this survey showed that wild sunflower exhibits geographically structured genetic variation, as samples from the Great Plains region of the central United States were genetically divergent from accessions from California and the southwestern United States. Sunflower populations from the Great Plains harbored greater allelic diversity than did wild sunflower from the western United States. Comparison of genetic variability in wild and domesticated sunflower by principal coordinate analysis showed these groups to be genetically divergent, in large part due to differences in the frequency of common alleles. Neighbor-Joining analyses of domesticated H. annuus, wild H. annuus and two closely related wild species (H. argophyllus T. & G. and H. petiolaris Nutt.) showed that domesticated sunflowers form a genetically coherent group and that wild sunflowers from the Great Plains may include the most likely progenitor of domesticated sunflowers. Received: 2 December 1996/Accepted: 4 April 1997     

Structure of genetic diversity in the two major gene pools of common bean (Phaseolus vulgaris L., Fabaceae)

Domesticated materials with well-known wild relatives provide an experimental system to reveal how human selection during cultivation affects genetic composition and adaptation to novel environments. In this paper, our goal was to elucidate how two geographically distinct domestication events modified the structure and level of genetic diversity in common bean. Specifically, we analyzed the genome-wide genetic composition at 26, mostly unlinked microsatellite loci in 349 accessions of wild and domesticated common bean from the Andean and Mesoamerican gene pools. Using a model-based approach, implemented in the software STRUCTURE, we identified nine wild or domesticated populations in common bean, including four of Andean and four of Mesoamerican origins. The ninth population was the putative wild ancestor of the species, which was classified as a Mesoamerican population. A neighbor-joining analysis and a principal coordinate analysis confirmed genetic relationships among accessions and populations observed with the STRUCTURE analysis. Geographic and genetic distances in wild populations were congruent with the exception of a few putative hybrids identified in this study, suggesting a predominant effect of isolation by distance. Domesticated common bean populations possessed lower genetic diversity, higher F _ST, and generally higher linkage disequilibrium (LD) than wild populations in both gene pools; their geographic distributions were less correlated with genetic distance, probably reflecting seed-based gene flow after domestication. The LD was reduced when analyzed in separate Andean and Mesoamerican germplasm samples. The Andean domesticated race Nueva Granada had the highest F _ST value and widest geographic distribution compared to other domesticated races, suggesting a very recent origin or a selection event, presumably associated with a determinate growth habit, which predominates in this race. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

中国普通菜豆形态性状分析及分类

对129份中国普通菜豆地方品种的形态性状进行分析,结果表明,8个性状共检测到35个变异类型,平均变异类型为4.375个,平均多态信息含量为0.5638。中国普通菜豆包括安第斯和中美两个基因库种质,中美洲基因库资源在参试资源中比重较大,但安第斯基因库资源遗传多样性水平高于中美基因库材料。由中美基因库向安第斯基因库渗透的天然杂交种质可为普通菜豆高产、优质、抗逆育种提供有价值的桥梁品种。     

Physiological and genetic analysis of root responsiveness to auxin-producing plant growth-promoting bacteria in common bean (Phaseolus vulgaris L.)

Plant root development can be largely affected through the association of roots with plant growth-promoting rhizobacteria (PGPR). However, little is known about the identity of plant genes enabling such PGPR-plant root associations. Differences in the responsiveness to PGPR among cultivars suggest genetic variation for this trait within germplasm. In this study, two genotypes of common bean (Phaseolus vulgaris L.), BAT477 and DOR364, were identified showing contrasting responsiveness in root development to inoculation with the PGPR Azospirillum brasilense Sp245. Inoculation with an A. brasilense Sp245 mutant strain strongly reduced in auxin biosynthesis or addition of increasing concentrations of exogenous auxin to the plant growth medium, indicated that the differential response to A. brasilense Sp245 among the bean genotypes is related to a differential response to the bacterial produced auxin. To further assess the role of the plant host in root responsiveness, a population of Recombinant Inbred Lines (RILs) of the DOR364×BAT477 cross was used to evaluate the efficacy of exogenous auxin on root development. We detected significant phenotypic variation among the RILs for basal root formation during germination upon addition of auxin to the growth medium. Genetic analysis revealed two quantitative trait loci (QTLs) associated with basal root responsiveness to auxin of which one explained 36% of the phenotypic variation among the RILs. This latter QTL mapped to the same location as a QTL for root tip formation at low P, suggesting that the host effect on root responsiveness to IAA interacts with specific root development. Also, significant correlations between basal root responsiveness to auxin and growth, root tips and root dry weight at low P were identified. To our knowledge, this is the first report on QTL detection for root responsiveness to auxin.     

Molecular cloning of Phaseolus vulgaris cDNA encoding proliferating cell nuclear antigen

A cDNA fragment encoding a common bean (Phaseolus vulgaris) proliferating cell nuclear antigen (PCNA) was isolated using rapid amplification of cDNA 3' end (3' RACE) method, cloned and sequenced. The nucleotide sequence of this clone contains an open reading frame of 798 nucleotides encoding a protein of 265 amino acids. Alignment of the common bean PCNA predicted sequence shows its high degree of identity with PCNA from other plant species. Analysis of PCNA content in the germinating embryos of common bean showed a decrease in the protein level after 60h of germination. Moreover, PCNA was not detected in the tested plant organs (root, stem, leaf and flower). The presence of PCNA in the germinating seeds and its absence from mature plants suggests that this protein plays a crucial role during early stages of plant development.     

Demographic factors shaped diversity in the two gene pools of wild common bean Phaseolus vulgaris L.

Wild common bean (Phaseolus vulgaris L.) is distributed throughout the Americas from Mexico to northern Argentina. Within this range, the species is divided into two gene pools (Andean and Middle American) along a latitudinal gradient. The diversity of 24 wild common bean genotypes from throughout the geographic range of the species was described by using sequence data from 13 loci. An isolation–migration model was evaluated using a coalescent analysis to estimate multiple demographic parameters. Using a Bayesian approach, Andean and Middle American subpopulations with high percentage of parentages were observed. Over all loci, the Middle American gene pool was more diverse than the Andean gene pool (π_sil=0.0089 vs 0.0068). The two subpopulations were strongly genetically differentiated over all loci (F_st=0.29). It is estimated that the two current wild gene pools diverged from a common ancestor ∼111 000 years ago. Subsequently, each gene pool underwent a bottleneck immediately after divergence and lasted ∼40 000 years. The Middle American bottleneck population size was ∼46% of the ancestral population size, whereas the Andean was 26%. Continuous asymmetric gene flow was detected between the two gene pools with a larger number of migrants entering Middle American gene pool from the Andean gene pool. These results suggest that because of the complex population structure associated with the ancestral divergence, subsequent bottlenecks in each gene pool, gene pool-specific domestication and intense selection within each gene pool by breeders; association mapping would best be practised within each common bean gene pool.     

Osmotic stress affects water relations, growth, and nitrogen fixation in Phaseolus vulgaris plants

The effects of mannitol-mediated osmotic stress on water relations, plant growth and symbiotic N₂-fixation in four common bean (Phaseolus vulgaris) lines (Coco Blanc, BAT 477, BRB 77 and Flamingo) were studied. After germination, seedlings were inoculated with a reference strain (Rhizobium tropici CIAT 899) and aerohydroponically grown in a glasshouse. Osmotic stress was applied by 50 mM mannitol. Plants were harvested 4 weeks after osmotic stress application. Measured parameters were plant water relations, growth, nodule development, and symbiotic N₂-fixation (SNF) as well as leghemoglobin contents. Osmotic stress induced significant changes in water relations, growth and symbiotic N₂-fixation in stressed plants compared to control ones in all lines studied. A noticeable different behaviour was observed in the end of the treatment: Flamingo was the most tolerant line, whereas Coco blanc was the most sensitive, the two other lines exhibited an intermediate behaviour. The four bean lines displayed significant differences in their responses to osmotic stress. This study indicated that the relative tolerance of Flamingo line seems to be due to its ability to maintain higher leaf water potential, adequate leaf area and abundant and efficient nodular system, which in turn determines an important rate of SNF.     

Determination of the population structure of common bean (Phaseolus vulgaris L.) accessions using lipoxygenase and resistance gene analog markers

The common bean (Phaseolus vulgaris L.) is an important food legume throughout the world. Because of the conservation across different plant species, it is possible to evaluate the degree of genetic diversity in the common bean using gene-based marker techniques. The lipoxygenase (LOX) and resistance gene analog (RGA) genes play an important role in the response to biotic and abiotic stresses. Eighty-six common bean accessions were genotyped using gene-based LOX and RGA markers. The total number of polymorphic bands ranged from 193 for LOX to 17 for RGA markers. We detected considerable diversity with a mean of 8.7 alleles per primer for the LOX analysis. For the RGA markers, the number of alleles per polymorphic locus varied from 1 to 4 with an average allele number of 2.8. The genetic similarity between the accessions based on the LOX and RGA markers ranged from 0.12 to 0.55. Using STRUCTURE, 3 groups were revealed among the accessions. The results of this study should provide valuable information for future studies on the genetic diversity of common bean accessions and for association mapping studies examining the relationships between the genotypic and phenotypic traits related to the stress response.     

普通菜豆种质资源表型鉴定及多样性分析

对646份普通菜豆核心种质在贵州毕节进行了表型鉴定,结果表明,普通菜豆具有丰富的形态性状多样性。总变异数为367,平均遗传丰富度为8.34,变异范围2~31;遗传多样性指数为0.63,变异范围为0.02~0.91。通过多变量的主成分分析,前3个主成分的贡献率较大,分别为17.73%、15.35%和11.33%。依据表型鉴定数据信息,将供试种质聚类并划分为4组。Ⅰ组的遗传多样性较高,主要为直立有限的大粒资源,大多资源属于安第斯基因库;Ⅱ组的遗传多样性最低,为直立无限生长习性的小粒资源,属于中美基因库;Ⅲ组的遗传多样性最高,主要以蔓生无限为主,包括小部分直立无限和匍匐无限的资源;Ⅳ组的遗传多样性较低,为蔓生无限生长习性、株高最高、分枝数最少的资源。筛选到大粒、多荚、长荚、宽荚等具有特异性状的种质资源35份。