Number of Experiments that Should be Considered in the Cluster Analysis of Common Bean Genotypes for Plant Architecture and Grain Yield Traits

The number of experiments that allows the choice of parents to be used in controlled crossings in a more assertive way in cluster analysis is unknown for plant architecture and grain yield traits in common bean. Therefore, the objective of this work was to determine the number of experiments that should be considered in Tocher's and the unweighted pair group method with arithmetic mean (UPGMA) cluster analyses to identify promising common bean parents for several plant architecture and grain yield traits. Four experiments were carried out in different years and growing seasons, in the same site. The randomized block design was used and 17 common bean genotypes with carioca (beige seed coat with brown streaks) and black grains were evaluated in relation to 12 traits related to plant architecture and five traits related to grain yield. Statistical analyses were performed with data obtained from individual and combined experiments. Significant genotype × experiment interaction was observed for most of the evaluated traits. When Tocher's and UPGMA cluster analyses was performed from data obtained in individual experiments different groups were formed. The use from data obtained in two, three ou four experiments allowed greather reliability in the formation of groups. Three and two experiments are sufficient in the Tocher's and the UPGMA cluster analyses, respectively, to identify promising carioca and black common bean parents for several plant architecture and grain yield traits in a more assertive way.

Genetic Diversity and Population Structure of Job’s Tears(Coix lacryma-jobi L.) Germplasm Based on ISSR Marker

Background: Job's tears（Coix lachryma-jobi L.）is a minor cereal and an important food item in some parts of Asia. It has also been used in the traditional Chinese medicine for relieving various ailments, therefore, it plays an important role in our lives. Lack of excellent new varieties hinders the development of coix as a sustainable crop, and it is urgent to provide new cultivars with excellent trait in Chinese Coix industry. Results: ISSR markers were used to assess the genetic diversity and population structure of 8 populations of Job’s tears in China. A genotyping analysis that utilized ten ISSR primer pairs resulted in the production of 116 bands, of which 98 were polymorphic. The Guizhou population (PPB = 81.90%, h = 0.3113, I = 0.4589) was the most genetically diverse, while the lowest was observed in the Hebei population (PPB = 46.55%, h = 0.1842, I = 0.2701). Genetic differentiation analyses including GST and AMOVA illustrated that genetic variation was most prevalent within populations while only minor variations were observed among populations. Genetic distance coefficients ranged from 0.0095 to 0.0948 for the 8 populations; the genetic relationship between the Guizhou and Chongqing populations was the closest, while the most distant genetic relationship occurred between the Hubei and Hunan populations. The results of an UPGMA cluster analysis that investigated genetic diversity among the populations were consistent with the genetic distance results. The results of a STRUCTURE analysis suggested that 94 Job’s tears accessions could be grouped into two subpopulations. Moreover, according to a cluster analysis based on the UPGMA for individuals of Job’s tears, accessions were divided into two major clusters. The results of the Bayesian cluster and UPGMA cluster analyses were largely consistent despite minor differences. There was no significant correlation between genetic distance and geographic distance (r = 0.055, p = 0.782). Conclusions: Our study was undertaken to systematically analyze genetic diversity and population structure in 94 Job’s tears accessions using ISSR markers. And this study provides us with valuable information pertaining to germplasm collection, genetic improvement, and systematic utilization of Job’s tears.

Genome-Wide Assessment of Avocado Germplasm Determined from Specific Length Amplified Fragment Sequencing and Transcriptomes: Population Structure, Genetic Diversity, Identification, and Application of Race-Specific Markers

Genomic data is a powerful tool. However, the phylogenetic relationships among different ecological races of avocado remain unclear. Here, we used the results from specific length amplified fragment sequencing (SLAF-seq) and transcriptome data to infer the population structure and genetic diversity of 21 avocado cultivars and reconstructed the phylogeny of three ecological races and two interracial hybrids. The results of the three analyses performed (unweighted pair-group methods with arithmetic means (UPGMA) cluster, Principal coordinate analysis (PCoA), and STRUCTURE) based on single nucleotide polymorphisms (SNPs) from SLAF-seq all indicated the existence of two populations based on botanical race: Mexican–Guatemalan and West Indian genotype populations. Our results based on SNPs from SLAF-seq indicated that the Mexican and Guatemalan races were more closely related to each other than either was to the West Indian race, which also was confirmed in the UPGMA cluster results based on SNPs from transcriptomic data. SNPs from SLAF-seq provided strong evidence that the Guatemalan, Mexican, and Guatemalan × Mexican hybrid accession possessed higher genetic diversity than the West Indian races and Guatemalan × West Indian hybrid accessions. Six race-specific Kompetitive allele specific PCR (KASP) markers based on SNPs from SLAF-seq were then developed and validated.

Screening for Eruca genotypes tolerant to polyethylene glycol-simulated drought stress based on the principal component and cluster analyses of seed germination and early seedling growth

Water deficit is an environmental factor that constrains crops to express their ecophysiological potential and causes crop yield reduction. Eruca vesicaria has been reported to be one of the most drought-tolerant species in Cruciferae. In this study, polyethylene glycol-simulated drought tolerance was evaluated in one line of Brassica carinata, one line of Brassica napus and 249 Eruca lines based on the principal component analysis (PCA) and unweighted pair-group arithmetic average (UPGMA) cluster analysis. The PCA based on eight drought tolerance indices indicated that the first three components accounted for 85.46% of the total variation, with principal component (PC) 1 accounting for 43.89%, PC2 for 27.85% and PC3 for 13.73% of the total variation. The UPGMA cluster analysis indicated that B. napus cultivar Zhongshuang 9 and Eruca lines could be clustered into five major groups, with group 1 being, in general, drought sensitive, group 2 being slightly–medium drought tolerant, group 3 being drought tolerant, group 4 being highly drought sensitive and group 5 being highly drought tolerant. B. carinata cultivar XB1, as an outstander, showed high drought sensitivity. The UPGMA cluster dendrogram provides a good representation of the similarity matrix (r= 0.68). The drought-tolerant Eruca materials obtained in this study will be valuable for genetic improvement not only in Eruca itself, but also in Brassica crops since they are drought-tolerant lines from a drought-tolerant species.

Identification of Rhus succedanea L. Cultivars Using Elliptic Fourier Descriptors Based on Fruit Shape

We have developed a method to identify cultivars of Rhus succedanea L. based on their fruit contour shape. For this, we collected fruits of five cultivars from three different environments (differing in site and/or year of collection) and the horizontal contour shape of each fruit was expressed by 37 elliptic Fourier descriptors, normalized in terms of size, rotation, shift and starting point of contour tracing. The first six components derived from a principal component analysis of the elliptic Fourier descriptors explained 89% of the variance. The differences among cultivars, environments and the cultivar x environment interaction were significant at the 0.01% probability level for all six principal components according to ANOVA. UPGMA cluster analysis based on the six principal components showed a high degree of clustering and most (but not all) ramets from the same cultivar clustered together. However, results of a UPGMA cluster analysis of Mahalanobis’ generalized distances among cultivars and environments, based on the 37 elliptic Fourier descriptors, showed that samples from the same cultivars clustered together, regardless of the environmental factors. We then applied a ‘similarity probability’ test, based on Mahalanobis’ generalized distances and a randomization test. The similarity probabilities between descriptors in the database and sampled fruits, when the cultivars they represented were included in the database, were >97%. In contrast, for samples representing cultivars that were not included in the database, the probabilities were <46%. These figures also apply to pairs of samples included in the database that represented the same cultivar, and different cultivars, respectively. These results suggest that it is possible to identify R. succedanea cultivars based on fruit contour shape using elliptic Fourier descriptors and similarity probability analysis.

Toxigenic diversity of two different RAPD groups ofStachybotrys chartarumisolates analyzed by potential for trichothecene production and for boar sperm cell motility inhibition

Thirty-one isolates of Stachybotrys chartarum from indoor and outdoor environments were analyzed for the presence of the trichodiene synthase (Tri5) gene, trichothecenes, boar sperm cell motility inhibition, and randomly amplified polymorphic DNA banding patterns (RAPDs). Twenty-two S. chartarum isolates tested positive for the Tri5 gene and nine were negative when tested using novel Tri5 gene-specific PCR primer pair. The Tri5 gene positive isolates contained satratoxins (five isolates) or the simple trichothecene, trichodermol (11 isolates). The Tri5 gene negative isolates did not produce satratoxins or trichodermol. Nineteen S. chartarum isolates, distributed among the Tri5 gene negative and positive groups, inhibited boar spermatozoan motility at concentrations of [Formula: see text]60 μg of crude cell extract/mL. The inhibition of motility was independent of satratoxins or atranones. Unweighted pair group method of arithmetic averages (UPGMA) cluster analysis of RAPD fragments clustered the 31 S. chartarum isolates in two distinct groups designated as RAPD groups 1 and 2. The grouping of S. chartarum isolates obtained by UPGMA cluster analysis of RAPD fragments was identical to the grouping obtained by Tri5 gene-specific PCR. This indicates that the S. chartarum isolates belonging to different groups were genetically distinct in a much wider area than just the Tri5 gene.Key words: boar sperm cell motility inhibition, RAPD, Stachybotrys chartarum, toxicity, trichothecene, trichodiene synthase (Tri5) gene.