Anatomical root variations in response to water deficit: wild and domesticated common bean (Phaseolus vulgaris L)

Root anatomical responses to water deficit are diverse and regulation of water uptake strongly depends on plant anatomy. The ancestors of common bean (Phaseolus vulgaris L.) cultivars are the wild common beans. Because wild beans adapt and survive well in the natural environment, it is hypothesized that wild common bean roots are less affected than those of domesticated beans at low substrate water potential (ψW). A wild common bean accession from Chihuahua Mexico and cv. Bayomex were studied. Seedlings with a mean root length between 3 and 4 cm were maintained for 24 h in vermiculite at ψW of -0.03 (well hydrated), -0.65, -1.48 and -2.35 MPa (partially dry). Ten anatomical characteristics of differentiation and cell division in root regions were evaluated. Thickness of epidermis and protoderm diminished similarly in wild and domesticated beans growing at low substrate ψW (between -0.65 and -2.35 MPa). At the same time, parenchymatic cell area diminished by 71 % in the domesticated variety, but by only 32 % in the wild bean at -2.35 MPa. The number of cells in the cortex and the thickness of the xylem wall increased in both wild and domesticated beans at low substrate ψW; nevertheless, the effect was significantly lower in the wild bean. The number of xylem vessels increased in the cultivar (up to 40 %) while in the wild bean it decreased (up to 33 %). The diameter of xylem vessels and transverse root area diminished (15 and 57 %, respectively) in the cultivar, but in the wild common bean were not affected. Anatomical root characteristics and their modifications in both differentiation and cell division in root regions demonstrated that the wild bean reacted quite differently to substrate ψW than the domesticated common bean.     

Phaseolin variability among wild and cultivated common beans (Phaseolus vulgaris) from Colombia

Phaseolin seed protein variability in a group of 8 wild and 77 cultivated common bean (Phaseolus vulgaris) accessions was determined using 1-dimensional SDS/ PAGE and 2-dimensional IEF-SDS/PAGE. Wild common bean accessions exhibited the 'CH' and 'B' patterns, previously undescribed among either wild or cultivated common beans. The cultivated genotypes showed (in decreasing frequency) the previously described 'S,' T,' and 'C phaseolin patterns as well as the new 'B' pattern similar to the pattern identified in a Colombian wild common bean accession. In the northeastern part of the Colombian bean-growing region, the cultivars exhibited almost exclusively an 'S' phaseolin type, while in the south-western part, the 'T' and 'C phaseolin cultivars were more frequent. Seed size analysis indicated that 'T' and 'C' phaseolin cultivars had larger seeds than 'S' and 'B' phaseolin cultivars. Our results suggest that Colombia is a meeting place for Andean and Middle American common bean germplasms, as well as a domestication center for the common bean.     

Detecting hybridization between wild species and their domesticated relatives

The widespread occurrence of free-ranging domestic or feral carnivores (dogs, cats) or ungulates (pigs, goats), and massive releases of captive-reproduced game stocks (galliforms, waterfowl) is raising fear that introgressive hybridization with wild populations might disrupt local adaptations, leading to population decline and loss of biodiversity. Detecting introgression through hybridization is problematic if the parental populations cannot be sampled (unlike in classical stable hybrid zones), or if hybridization is sporadic. However, the use of hypervariable DNA markers (microsatellites) and new statistical methods (Bayesian models), have dramatically improved the assessment of cryptic population structure, admixture analyses and individual assignment testing. In this paper, I summarize results of projects aimed to identify occurrence and extent of introgressive hybridization in European populations of wolves (Canis lupus), wildcats (Felis silvestris), rock partridges and red-legged partridges (Alectoris graeca and Alectoris rufa), using genetic methods. Results indicate that introgressive hybridization can be locally pervasive, and that conservation plans should be implemented to preserve the integrity of the gene pools of wild populations. Population genetic methods can be fruitfully used to identify introgressed individuals and hybridizing populations, providing data which allow evaluating risks of outbreeding depression. The diffusion in the wild of invasive feral animals, and massive restocking with captive-reproduced game species, should be carefully controlled to avoid loss of genetic diversity and disruption of local adaptations.     

Genetic structure and differentiation of wild and domesticated populations of Capsicum annuum (Solanaceae) from Mexico

 Genetic variation and structure of ten wild, three domesticated and one wild-cultivated populations of pepper (Capsicum annuum) from northwestern Mexico were studied in order to find out if the domestication process has reduced the genetic variation of the modern cultivars of this species. The analysis was based on 12 polymorphic loci from nine isozymes. Wild populations were sampled in different habitats along a latitudinal gradient of ca. 500 km. All populations had high genetic variation (i.e. wild: A = 2.72, P = 90.8%, He = 0.445; wild-cultivated: A = 2.50, P = 92.3%, He = 0.461; domesticated: A = 2.60, P = 84.6%, He = 0.408), indicating little genetic erosion in modern cultivars of pepper. Genetic diversity estimated by Nei's method showed that most genetic variation is found within, rather than among populations. However, genetic differentiation is greater among cultivated (G _ST=0.167) than among wild (G _ST=0.056) populations. Wild populations had an average genetic identity (I) of 0.952, indicating little differentiation and high gene flow (Nm=4.21) among these populations. Average genetic identity between wild and domesticated populations was of I=0.818, revealing that the domestication process has modified the genetic composition of commercial varieties of pepper. Changes in genetic composition among commercial varieties seem to have occurred in different directions, as indicated by the average value of I = 0.817 among these populations. The high level of diversity found in wild populations of C. annuum suggests that the wild relatives of cultivated peppers are a valuable genetic resource which must be conserved. Received May 5, 1999 Accepted October 30, 2000     

Multiple origins of the determinate growth habit in domesticated common bean (Phaseolus vulgaris)

Background and Aims

The actual number of domestications of a crop is one of the key questions in domestication studies. Answers to this question have generally been based on relationships between wild progenitors and domesticated descendants determined with anonymous molecular markers. In this study, this question was investigated by determining the number of instances a domestication phenotype had been selected in a crop species. One of the traits that appeared during domestication of common bean (Phaseolus vulgaris) is determinacy, in which stems end with a terminal inflorescence. It has been shown earlier that a homologue of the arabidopsis TFL1 gene – PvTFL1y – controls determinacy in a naturally occurring variation of common bean.

Methods

Sequence variation was analysed for PvTFL1y in a sample of 46 wild and domesticated accessions that included determinate and indeterminate accessions.

Key Results

Indeterminate types – wild and domesticated – showed only synonymous nucleotide substitutions. Determinate types – observed only among domesticated accessions – showed, in addition to synonymous substitutions, non-synonymous substitutions, indels, a putative intron-splicing failure, a retrotransposon insertion and a deletion of the entire locus. The retrotransposon insertion was observed in 70 % of determinate cultivars, in the Americas and elsewhere. Other determinate mutants had a more restricted distribution in the Americas only, either in the Andean or in the Mesoamerican gene pool of common bean.

Conclusions

Although each of the determinacy haplotypes probably does not represent distinct domestication events, they are consistent with the multiple (seven) domestication pattern in the genus Phaseolus. The predominance of determinacy in the Andean gene pool may reflect domestication of common bean prior to maize introduction in the Andes.     

Purification and properties of cellulase from Phaseolus vulgaris

Cotyledons of germinating kidney beans contain two forms of a carboxy methyl cellulase which can be separated by ammonium sulfate fractionation and isoelectric focusing. The two cellulases are similar in their molecular weight but differ in isoelectric points, pH and temperature optimum, pH and temperature stability and sensitivity to thiol inhibitors and metal ions. One cellulase (isoelectric point 4.8) has been purified 100-fold to give a major protein band on acrylamide gel electrophoresis.     

Asymmetry of gene flow and differential geographical structure of molecular diversity in wild and domesticated common bean (<Emphasis Type="Italic">Phaseolus vulgaris</Emphasis> L.) from Mesoamerica

Using amplified fragment length polymorphisms (AFLPs), we analyzed the genetic structure of wild and domesticated common bean (Phaseolus vulgaris L.) from Mesoamerica at different geographical levels to test the hypothesis of asymmetric gene flow and investigate the origin of weedy populations. We showed both by phenetic and admixture population analyses that gene flow is about three- to four-fold higher from domesticated to wild populations than in the reverse direction. This result, combined with other work, points to a displacement of genetic diversity in wild populations due to gene flow from the domesticated populations. The weedy populations appear to be genetically intermediate between domesticated and wild populations, suggesting that they originated by hybridization between wild and domesticated types rather than by escape from cultivation. In addition, the domesticated bean races were genetically similar confirming a single domestication event for the Mesoamerican gene pool. Finally, the genetic diversity of the domesticated bean population showed a lower level of geographic structure in comparison to that of the wild populations.     

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     

A genome-wide scan for signatures of directional selection in domesticated pigs

Background

Animal domestication involved drastic phenotypic changes driven by strong artificial selection and also resulted in new populations of breeds, established by humans. This study aims to identify genes that show evidence of recent artificial selection during pig domestication.

Results

Whole-genome resequencing of 30 individual pigs from domesticated breeds, Landrace and Yorkshire, and 10 Asian wild boars at ~16-fold coverage was performed resulting in over 4.3 million SNPs for 19,990 genes. We constructed a comprehensive genome map of directional selection by detecting selective sweeps using an F_ST-based approach that detects directional selection in lineages leading to the domesticated breeds and using a haplotype-based test that detects ongoing selective sweeps within the breeds. We show that candidate genes under selection are significantly enriched for loci implicated in quantitative traits important to pig reproduction and production. The candidate gene with the strongest signals of directional selection belongs to group III of the metabolomics glutamate receptors, known to affect brain functions associated with eating behavior, suggesting that loci under strong selection include loci involved in behaviorial traits in domesticated pigs including tameness.

Conclusions

We show that a significant proportion of selection signatures coincide with loci that were previously inferred to affect phenotypic variation in pigs. We further identify functional enrichment related to behavior, such as signal transduction and neuronal activities, for those targets of selection during domestication in pigs.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1330-x) contains supplementary material, which is available to authorized users.     

Linkage Analysis of Hydroxyproline-poor Glycoprotein from Phaseolus vulgaris

Hydroxyproline-poor glycoprotein contains a single polypeptide chain with lysine at the N-terminus. Removal of carbohydrate attached to serine by alkali treatment produces two polypeptide fractions. Labeling with ³⁵S indicates that most serine residues having a carbohydrate substituent removed by alkali occur on the polypeptide fraction of lower molecular weight. Following alkali treatment, two additional N-terminal amino acids, proline and glycine, were detected suggesting that alkali treatment also cleaves peptide bonds. Methylation analysis of native and degraded glycoproteins, extracted 24, 27, and 36 hours after wounding, demonstrates the following structural features of carbohydrate attached to serine. Arabinose may be (1 → 2)-, (1 → 3)-, or (1 → 5)-linked, glucose occurs as a chain of β-(1 → 4)-linked residues, and galactose occurs as a nonreducing terminal unit.     

Fertile,intermediate hybrids between Phaseolus vulgaris and P. acutifolius from congruity backcrossing

Summary Recurrent or introgressive backcrossing of Phaseolus vulgaris — P. acutifolius hybrids with either P. vulgaris or P. acutifolius increased fertility, as measured by pollen stainability and seed per pod from non-manipulated flowers, while invariably resulting in loss of traits from the non-recurrent parent. When hybrids were backcrossed with each of the parent species in alternate generations (congruity backcrossing), fertility decreased in early generations but gradually increased in later generations. By the fourth or fifth generation, congruity-backcross hybrids produced numbers of seeds per pod from non-manipulated flowers comparable to those of parent species, although the percent of stainable pollen tended to be lower. Congruity-backcross hybrids were intermediate to parent species when pedigrees contained equal representation of parents but favored the majority parent when pedigrees were unbalanced. Individuals exhibiting symptoms of developmental incongruity, such as abnormal leaflet number, foliar variagation, or unusual growth patterns, occurred in each generation. However, completely new characteristics appeared after the second backcross generation, presumably due to recombination. Backcrossing to both parent species in alternate generation reversed incongruity, allowing selection for fertility without loss of traits from one of the parent species.Scientific Journal Series Paper Number 15, 671 of the Minnesota Agricultural Experimental Station     

Sodium Recirculation and Loss from Phaseolus vulgaris L.

In a split-root experiment, ²²Na was supplied to Phaseolus vulgarisL. roots emerging from the stem, 2.5 cm above the main roots.Sodium exported from these upper roots was translocated a shortdistance upward in the stem and downward to the main roots.Most of the ²²Na arriving in the main roots was lost to themedium. Sodium loss from P. vulgaris roots into KCI or NaCl was similarand was not affected by oligomycin. The results confirm a previous hypothesis regarding the mechanismof sodium exclusion from the tops of sodium non-accumulatorplants. Phaseolus vulgaris L., bean, sodium transport     

New isoflavonoids related to kievitone from Phaseolus vulgaris

The new isoflavonoids 5,7,2′,4′-tetrahydroxy-8-(3,3-dimethylallyl)isoflavone (2,3-dehydrokievitone) and 7,2′,4′-trihydroxy-8-(3,3-dimethylallyl)isoflavanone (5-deoxykievitone) have been isolated from fungus-inoculated Phaseolus vulgaris pod tissue and from the inoculation droplets. A third isoflavonoid was tentatively identified as 1″,2″-dehydrocyclokievitone and appears to be a metabolite of the phytoalexin kievitone.     

Rhythms of volatiles release from healthy and insect-damaged Phaseolus vulgaris

The release rhythm of volatiles is an important physiological characteristic of plants, because the timing of release can affect the function of each particular volatile compound. However, most studies on volatiles release rhythms have been conducted using model plants, rather than crop plants. Here, we analyzed the variations in volatile compounds released from healthy and leafminer (Liriomyza huidobrensis)-infested kidney bean (Phaseolus vulgaris), an important legume crop plant, over a 24 h period. The constituents of the volatiles mixture released from plants were analyzed every 3 h starting from 08:00. The collected volatiles were identified and quantified by gas chromatography–mass spectrometry. Undamaged kidney bean plants released trace amounts of volatiles, with no obvious release rhythms. However, leafminer-damaged plants released large amounts of volatiles, in two main peaks. The main peak of emission was from 17:00 to 20:00, while the secondary peak was in the early morning. The terpene volatiles and (Z)-3-hexenyl acetate showed similar rhythms as that of total volatiles. However, the green leaf volatile (Z)-3-hexen-ol was emitted during the night with peak emission in the early morning. These results give us a clear picture of the volatiles release rhythms of kidney bean plants damaged by leafminer.Keywords : green leaves volatiles, Liriomyza huidobrensis, rhythm, terpene, (Z)-3-hexen-ol