Genetic architecture of chalcone isomerase non-coding regions in common bean (Phaseolus vulgaris L.).

Sequence data for 2 non-coding regions of the chalcone isomerase gene were analyzed to study the genetic architecture of common bean (Phaseolus vulgaris L.). One region corresponded to the first 596 nucleotides (nt) of the 5'-untranslated region (UTR). The other region was the 710 nt intron 3. Data were collected from 67 genotypes representing both landraces and cultivars from the geographical range of the cultivated form of the species. Variability in the 5'-UTR region was represented by single nucleotide polymorphisms (SNPs), whereas intron 3 variation was due to a collection of SNPs and insertion-deletion events. Diversity was greater in the 5'-UTR (pi = 0.0175) than in intron 3 (pi = 0.0089). For each region, diversity was greater for genotypes of Middle American than Andean origin. A single recombination event was observed, and the hybridization pattern necessary to derive the recombinant genotypes supported the previous observation of an ancestral gene pool from which modern domesticated genotypes are derived. For both regions, a strongly supported Andean group was observed, whereas the presence of 2 Middle American subgroups was also supported. Although a significantly positive Tajima's D statistic was observed for the 5'-UTR for all genotypes, we conclude that this is more likely the result of a strong demographic effect and that balancing selection is occurring only among the Middle American genotypes.     

Comparison of common bean (Phaseolus vulgaris L.) genotypes for nitrogen fixation tolerance to soil drying

Aims

Common bean is a major source of protein for many people worldwide. However, the crop is often subjected to drought conditions and its advantage in undertaking symbiotic nitrogen fixation can be severely decreased. The primary objective of this study was to compare the resistance of nitrogen fixation of 12 selected genotypes to soil drying.

Methods

Twelve common bean genotypes of diverse genetic background were compared. Plants were grown in pots and subjected to soil drying over about 2 weeks. Nitrogen fixation was measured daily using a flow-through acetylene reduction technique. The plants were exposed to acetylene for only a short time period allowing repeated measures. The acetylene reduction rate of plants on drying soil was normalized against the rates measured for well-watered plants.

Results

Substantial variability was identified among genotypes in the threshold soil water content at which nitrogen fixation was observed to decrease. Genotypes SER 16, SXB 412, NCB 226, and Calima were found to have the greatest delay in their decrease in nitrogen fixation rates based on soil water content. These four genotypes expressed substantial tolerance of nitrogen fixation to soil drying. These experiments also resulted in data on the threshold soil water contents at which transpiration rates decreased. A decrease in transpiration rates at high soil water contents is potentially advantageous since it allows soil water conservation for use as the severity of the drought increases. There was a general trend of those genotypes with sustained nitrogen fixation rates to low soil water contents also expressing decreased transpiration rates at high soil water contents.

Conclusions

This study identified genetic variation among common bean genotypes in their response of nitrogen fixation and transpiration to soil drying. Five genotypes (SER 16, SXB 412, NCB 226, Calima, and SEA 5) expressed the desired traits for water-limited conditions, which might be exploited in breeding efforts.     

Microsatellite marker diversity in common bean (Phaseolus vulgaris L.)

A diversity survey was used to estimate allelic diversity and heterozygosity of 129 microsatellite markers in a panel of 44 common bean (Phaseolus vulgaris L.) genotypes that have been used as parents of mapping populations. Two types of microsatellites were evaluated, based respectively on gene coding and genomic sequences. Genetic diversity was evaluated by estimating the polymorphism information content (PIC), as well as the distribution and range of alleles sizes. Gene-based microsatellites proved to be less polymorphic than genomic microsatellites in terms of both number of alleles (6.0 vs. 9.2) and PIC values (0.446 vs. 0.594) while greater size differences between the largest and the smallest allele were observed for the genomic microsatellites than for the gene-based microsatellites (31.4 vs. 19.1 bp). Markers that showed a high number of alleles were identified with a maximum of 28 alleles for the marker BMd1. The microsatellites were useful for distinguishing Andean and Mesoamerican genotypes, for uncovering the races within each genepool and for separating wild accessions from cultivars. Greater polymorphism and race structure was found within the Andean gene pool than within the Mesoamerican gene pool and polymorphism rate between genotypes was consistent with genepool and race identity. Comparisons between Andean genotypes had higher polymorphism (53.0%) on average than comparisons among Mesoamerican genotypes (33.4%). Within the Mesoamerican parental combinations, the intra-racial combinations between Mesoamerica and Durango or Jalisco race genotypes showed higher average rates of polymorphism (37.5%) than the within-race combinations between Mesoamerica race genotypes (31.7%). In multiple correspondance analysis we found two principal clusters of genotypes corresponding to the Mesoamerican and Andean gene pools and subgroups representing specific races especially for the Nueva Granada and Peru races of the Andean gene pool. Intra population diversity was higher within the Andean genepool than within the Mesoamerican genepool and this pattern was observed for both gene-based and genomic microsatellites. Furthermore, intra-population diversity within the Andean races (0.356 on average) was higher than within the Mesoamerican races (0.302). Within the Andean gene pool, race Peru had higher diversity compared to race Nueva Granada, while within the Mesoamerican gene pool, the races Durango, Guatemala and Jalisco had comparable levels of diversity which were below that of race Mesoamerica.     

Inheritance of partial resistance to bean rust in the common bean (Phaseolus vulgaris L.)

The inheritance of partial resistance within eight bean cultivars to a single-pustule isolate of bean rust was studied by means of a F₁ diallel test. General combining ability (GCA) and specific combining ability (SCA) were very highly significant over two seasons and in interaction with seasons. The partitioning of the sums of squares indicated the greater importance of GCA in the inheritance of the resistance. Reciprocal effects were not significant. The estimates of narrow-sense heritability in the two seasons were 0.899 ± 0.056 and 0.603 ± 0.065.     

Multiple paternity in common bean (Phaseolus vulgaris L., Fabaceae)

We report on two field experiments that were conducted in 1991 and 1992 at the South Coast Extension and Research Center, Irvine, CA, to study the incidence of multiple paternity in the common bean (Phaseolus vulgaris L.). Hypocotyl color and shikimate dehydrogenase (Skdh) isozymes were used as genetic markers. The white-seeded cultivar ‘Ferry Morse 53’ (FM 53) was used as the female parent. This cultivar is homozygous recessive (pp) for hypocotyl color. The pollen source parents were three homozygous dominant (PP) purple-hypocotyled, black-seeded cultivars. Three cultivars, ‘ICA Pijao,’ G4459, and the maternal parent FM 53, are of Mesoamerican origin and homozygous for the fast (F) allele at the Skdh locus. The other cultivar, Black Valentine, is of Andean origin and is homozygous for the slow (S) allele at the Skdh locus. Overall, 6 125 pods were obtained from 57 and 111 plants harvested individually in 1991 and 1992, respectively. All progeny, 28938 seeds, were scored for hypocotyl color at the seedling stage. The purple-hypocotyled seedlings were genotyped for the Skdh locus to identify their pollen parents. Multiple paternity was identified in all the pods with hybrid seeds (i.e., those of intercultivar crosses) at 5.8% and 8.1% in 1991 and 1992, respectively. All multiply sired pods produced both nonhybrid and hybrid seeds. As many as three successful fathers per pod were identified, but the number of markers limited measuring higher levels of multiple paternity. Most multiply sired pods (≈70%) were filled by nonhybrid seeds plus a single hybrid seed. Ovule position effect within multiply sired pods was inferred from the nonrandom distribution of hybrid seeds within a pod. On average, hybrid seeds occurred more frequently in ovules in position 7 (most basal) and in position 1 (most stylar) than in ovules in the middle positions of the pod.     

Distribution of nitrogen in common bean (Phaseolus vulgaris L.) genotypes selected for differences in nitrogen fixation ability

The improvement of N₂ fixation in legumes may lead to increased yields and reduced fertilizer requirement. Levels of N₂ fixation were determined for three cultivars and nine progeny lines from two inbred backcross common bean (Phaseolus vulgaris L.) populations that were grown at Hancock, Wissconsin in 1984 and 1985 using ¹⁵N-depleted (NH₄)₂SO₄. The high N₂-fixing line Puebla 152 was the donor parent for both inbred backcross populations and the cultivars Porrillo Sintetico and Sanilac were the recurrent parents for populations 21 and 24, respectively. Total N yield, fixed N₂ and % N derived from the atmosphere were determined for whole plants and plant parts at the R3 (50% bloom) and R9 (maturity) growth stages. Significant year-by-line interactions were found for N₂ fixation traits among the population 21 lines and parents, but not for population 24 lines and their parents. Measures of N₂ fixation at R3 were inadequate to predict N₂ fixation at R9. Population 24 lines and parents differed for N₂ fixation ability at R9, and fixed N₂ was correlated with maturity. The recovery of an inbred backcross progeny line, 24-21, which matured earlier and fixed more N₂ than the recurrent parent Sanilac indicated that N₂ fixation was heritable and that favorable alleles, independent of maturity, were recovered from a late-maturing, high N₂-fixing donor parent by utilizing the inbred backcross breeding method. Since most fixed N₂ and non-fixed N (>80%) was found in the seeds at maturity, and most lines did not vary for the distribution of nitrogen throughout the plant, selection for improved remobilization of nitrogen to the seed to increase yield is impractical in this genetic material. The highest N₂-fixing lines tended to have high and similar % Ndfa in all plant parts.     

Nodule conductance varied among common bean (Phaseolus vulgaris) genotypes under phosphorus deficiency

Common bean genotypes BAT477, COCOT, DOR364, Flamingo, and NAG310 were inoculated with Rhizobium tropici CIAT899 and grown under phosphorus deficiency. This treatment induced a significant decrease in shoot and nodule growth that varied among genotypes from 35% to 57% and from 45% to 61%, respectively, whereas root biomass was less affected. Phosphorus deficiency affected differently the genotypes for nodule number and size, and the responses of nodulated-root O2 uptake (Conr) to raising rhizospheric PO2. From the later data, nodule conductance could be computed by dividing the slope of the regression of Conr as a function of external pO2 by nodule surface area. It is concluded that differences in nodule conductance are related to genotypic tolerance to P deficiency.     

The effect of phosphorus availability on the carbon economy of contrasting common bean (Phaseolus vulgaris L.) genotypes

A common response to low phosphorus availability is increased relative biomass allocation to roots. The resulting increase in root:shoot ratio presumably enhances phosphorus acquisition, but may also reduce growth rates by diverting carbon to the production of heterotrophic rather than photosynthetic tissues. To assess the importance of increased carbon allocation to roots for the adaptation of plants to low P availability, carbon budgets were constructed for four common bean genotypes with contrasting adaptation to low phosphorus availability in the field ("phosphorus efficiency"). Solid-phase-buffered silica sand provided low (1 microM), medium (10 microM), and high (30 microM) phosphorus availability. Compared to the high phosphorus treatment, plant growth was reduced by 20% by medium phosphorus availability and by more than 90% by low phosphorus availability. Low phosphorus plants utilized a significantly larger fraction of their daytime net carbon assimilation on root respiration (c. 40%) compared to medium and high phosphorus plants (c. 20%). No significant difference was found among genotypes in this respect. Genotypes also had similar rates of P absorption per unit root weight and plant growth per unit of P absorbed. However, P-efficient genotypes allocated a larger fraction of their biomass to root growth, especially under low P conditions. Efficient genotypes had lower rates of root respiration than inefficient genotypes, which enabled them to maintain greater root biomass allocation than inefficient genotypes without increasing overall root carbon costs.     

Selection for increased nodule number in common bean (Phaseolus vulgaris L.)

Common bean (Phaseolus vulgaris L.) plants were grown for 21–28 days in plastic container-modified Leonard jar assemblies and placed in a controlled-environment room. The nodules on each plant were removed, counted; selected plants were repotted, grown and intercrossed to produce progenies for the next cycle of recurrent selection. Among the ten parent lines, Puebla 152 and WBR 22–34 produced the most nodules and Rio Tibagi and Negro Argel the fewest, when averaged over five experiments. An analysis of number of nodules on F₁ plants resulting from crosses made in a partial diallel design among the ten parents revealed highly significants variation for general combining ability (GCA) but not for specific combining ability (SCA). After three cycles of recurrent selection for nodule number per plant, the mean nodule number was 211% of the mean for the 10 parents control. Total nodule weight on selected plants also increased, but individual nodule weight decreased. Nineteen C₁ and 18 C₂ lines resulting from the individual plants selected for greater nodule number, along with the ten parents and two non-nodulating soybean lines included as non-fixing check plants were grown in a single experiment in a low-N field. C₂ lines on average accumulated significantly more N per plant than either the parents or C₁ lines, providing evidence for increased N₂ fixation measured by the N difference method. These data show that more nodules, possibly resulting from greater susceptibility to nodulation, are an important, heritable component of symbiosis and that selection for increased nodule number resulted in lines capable of fixing more atmospheric N₂.     

菜豆种质资源抗普通细菌性疫病鉴定

采用针刺叶片接种法、温室地面水层保湿方式,对146份普通菜豆种质资源进行抗普通细菌性疫病鉴定和评价,结果表明,该接种方法简便实用,保湿方式效果良好,鉴定结果准确;从146份普通菜豆种质中筛选出抗病种质(R)2份、中抗(MR)种质50份、感病(S)种质81份、高感种质(HS)13份。本研究表明针刺叶片接种、温室地面水层自然蒸发保持湿度可以作为大规模菜豆抗普通细菌性疫病鉴定的适宜方法。     

Monosomics in common bean,Phaseolus vulgaris

Summary Two monosomics of Phaseolus vulgaris (2n = 22) were found among selfed progeny of plants treated with colchicine. The monosomic chromosomes involved were identified as chromosomes H and J according to the previously suggested Giemsa karyotype. Both monosomic plants had slower growth rate and smaller size as compared with their respective euploid sibs. However, no apparent morphological characteristics distinguished the two monosomics. The frequencies of transmission through selfing of monosomics H and J were 9% and 10 % respectively.     

2-DE-based proteomic analysis of common bean (Phaseolus vulgaris L.) seeds

Common bean (Phaseolus vulgaris L.) is the most important grain legume for direct human consumption. Proteomic studies in legumes have increased significantly in the last years but few studies have been performed to date in P. vulgaris. We report here a proteomic analysis of bean seeds by two-dimensional electrophoresis (2-DE). Three different protein extraction methods (TCA-acetone, phenol and the commercial clean-up kit) were used taking into account that the extractome can have a determinant impact on the level of quality of downstream protein separation and identification. To demonstrate the quality of the 2-DE analysis, a selection of 50 gel spots was used in protein identification by mass spectrometry (MALDI-TOF MS and MALDI-TOF/TOF). The results showed that a considerable proportion of spots (70%) were identified in spite of incomplete genome/protein databases for bean and other legume species. Most identified proteins corresponded to storage protein, carbohydrate metabolism, defense and stress response, including proteins highly abundant in the seed of P. vulgaris such as the phaseolin, the phytohemagglutinin and the lectin-related α-amylase inhibitor.     

Sensitivity of the common bean (Phaseolus vulgaris L.) symbiosis to high soil temperature

Summary Experiments were done to test whether N fixation is more sensitive to high soil temperatures in common bean than in cowpea or soybean. Greenhouse experiments compared nodulation, nitrogenase activity, growth and nitrogen accumulation of several host/strain combinations of common bean with the other grain legumes and with N-fertilization, at various root temperatures. Field experiments compared relative N-accumulation (in symbiotic relative to N-fertilized plants) of common bean with cowpea under different soil thermal regimes. N-fertilized beans were unaffected by the higher temperatures, but nitrogen accumulation by symbiotic beans was always more sensitive to high root temperatures (33°C, 33/28°C, 34/28°C compared with 28°C) than were cowpea and soybean symbiosis. Healthy bean nodules that had developed at low temperatures functioned normally in acetylene reduction tests done at 35°C. High temperatures caused little or no suppression of nodule number. However, bean nodules produced at high temperatures were small and had low specific activity. ForP. vulgaris some tolerance to high temperature was observed among rhizobium strains (e.g., CIAT 899 was tolerant) but not among host cultivars. Heat tolerance ofP. acutifolius andP. lunatus symbioses was similar to that of cowpea and soybean. In the field, high surface soil temperatures did not reduce N accumulation in symbiotic beans more than in cowpea, probably because of compensatory nodulation in the deeper and cooler parts of the soil.     

Generation means analysis of climbing ability in common bean (Phaseolus vulgaris L.)

Climbing common bean (Phaseolus vulgaris L.) genotypes have among the highest yield potential of all accessions found in the species. Genetic improvement of climbing beans would benefit from an understanding of the inheritance of climbing capacity (made up of plant height [PH] and internode length [IL] traits). The objective of this study was to determine the inheritance of climbing capacity traits in 3 crosses made within and between gene pools (Andean x Andean [BRB32 x MAC47], Mesoamerican x Mesoamerican [Tío Canela x G2333], and Mesoamerican x Andean [G2333 x G19839]) using generation means analysis. For each population, we used 6 generations (P(1), P(2), F(1), F(2), BC(1)P(1), and BC(1)P(2)) that were evaluated at 2 growth stages (40 and 70 days after planting). Results showed the importance of additive compared with the dominant-additive portion of the genetic model. Broad-sense heritabilities for the traits varied from 62.3% to 85.6% for PH and from 66.5% to 83.7% for IL. The generation means analysis and estimates of heritability suggested that the inheritance of PH and IL in climbing beans is relatively simple.     

Environmental response patterns in commercial classes of common bean (Phaseolus vulgaris L.)

Summary The yield data of 39 cultivars of diverse commercial classes of beans (Phaseolus vulgaris L.) planted in seven locations in Michigan were subjected to cluster and canonical variate analyses. The essential findings and conclusions can be summarized as follows: (1) Cluster analysis classified the cultivars into sub-sets or clusters almost identically coinciding with their commercial class designation. Canonical variate analysis completely confirmed the sub-groupings. Within class similarities were attributed to a narrow genetic base resulting from a common genetic relationship, or at least sharing of a common gene pool. (2) It was found that two clusters could possess almost identical mean (cluster mean) yields, and deviate in opposite directions over the same range of environments. (3) When total genotype × environmental interaction variance was partitioned into between and within clusters, the cluster × environment portion constituted 80% of the total. (4) These results imply that if the behavior of a given cultivar across a series of environments is known, the behavior of all other members of the class across a similar range of environments would be predictable.Journal Article No. 10329 of the Michigan Agricultural Experiment Station     

Molecular diversity in Ligurian local races of common bean (Phaseolus vulgaris L.)

Abstract

Eight varieties of Ligurian common beans (Phaseolus vulgaris L.) were analysed using molecular approaches. Results were compared with two commercial cultivars (‘Cannellino’ and ‘Borlotto’). Data suggest that all Ligurian bean varieties have a low genetic variability and are very close to the commercial varieties. In particular, the three ‘Bianco’ varieties showed a molecular affinity, probably due to their common genomic origin.     

Genetic diversity of common bean (Phaseolus vulgaris L.) nodulating rhizobia in Nepal

Background and Aims

This study was conducted to reveal the genetic diversity of common bean (Phaseolus vulgaris L.) nodulating rhizobia in various agroecological regions in Nepal.

Method

A total of 63 strains were isolated from common bean grown in the soils collected from seven bean fields in Nepal and characterized based on the partial sequences of 16S–23S internal transcribed spacer (ITS) regions, 16S rDNA, nodC, and nifH. Symbiotic properties of some representative strains with host plants were examined to elucidate their characteristics in relation to genotype and their origin.

Results

The isolated strains belonged to Rhizobium leguminosarum, Rhizobium etli, Rhizobium phaseoli, and one unknown Rhizobium lineage, all belonging to a common symbiovar (sv.) phaseoli. Nine ITS genotypes were detected mainly corresponding to a single site, including a dominant group at three sites harboring highly diverse multiple ITS sequences. Three symbiotic genotypes corresponded to a geographical region, not to the ribosomal DNA group, suggesting horizontal transfer of symbiotic genes separately in each region. Great differences in nitrogenase activity and nodule forming ability among the strains irrespective of their species and origin were observed.

Conclusions

Nepalese Himalaya harbor phylogenetically highly diverse and site-specific strains of common bean rhizobia, some of which could have high potential of symbiotic nitrogen fixation.     

Time course of N2 fixation in common bean (Phaseolus vulgaris L.)

Field and greenhouse experiments were conducted to assess the nitrogen fixation rates of four cultivars of common bean (Phaseolus vulgaris L.) at different growth stages. The ¹⁵N isotope dilution technique was used to quantify biological nitrogen fixation. In the greenhouse, cultivars M4403 and Kallmet accumulated 301 and 189 mg N plant^–1, respectively, up to 63 days after planting (DAP) of which 57 and 43% was derived from atmosphere. Under field conditions, cultivars Bayocel and Flor de Mayo RMC accumulated in 77 DAP, 147 and 135 kg N ha^–1, respectively, of which approximately one-half was derived from the atmosphere. The rates of N₂ fixation determined at different growth stages increased as the plants developed, and reached a maximum during the reproductive stage both under field and greenhouse conditions. Differences in translocation of N were observed between the cultivars tested, particularly under field conditions. Thus, the fixed N harvest index was 93 and 60 for cultivars Flor de Mayo and Bayocel, respectively. In early stages of growth, the total content of ureides in the plants correlated with the N fixation rates. The findings reported in the present paper can be used to build a strategy for enhancing biological N₂ fixation in common bean.