Yield stability of determinate and indeterminate dry bean cultivars

Summary Yield stability of determinate and indeterminate dry bean (Phaseolus vulgaris L.) cultivars was compared using regression of genotypic performance on environmental means. Yields of 28 dry bean cultivars differing in plant growth habit and commercial class designation were obtained from 42 Michigan performance nurseries over the 6 year period 1980 to 1985. The determinate type I large-seeded kidney and cranberry bean cultivars had below-average seed yield and large mean square deviations from regression. Lower yielding determinate small-seeded navy cultivars had low deviation mean square values, while higher yielding determinate navy cultivars had correspondingly higher mean square deviations from regression. Although seed yield of cultivars with an indeterminate growth habit was greater than determinate cultivars, prostrate type III indeterminate cultivars had deviation mean square values equivalent to those of large-seeded determinate cultivars. The erect, short vine type II indeterminate cultivars (architypes) had greater than average seed yields and minimum deviations from regression. Compared with other plant types, the architype group showed a greater yield response to more productive environments, with regression coefficient values significantly greater than unity. These results indicate that the type II growth habit offers the breeder the best opportunity of obtaining greater seed yield without incurring loss of yield stability as occurs with the type I and type III growth habits. Since the dry bean cultivars utilized in this study represent two distinct centers of domestication, the regression analysis suggests that cultivars from the predominant genetic center demonstrate more yield stability. A non-significant rank correlation coefficient between the combined and separate analyses for deviation mean square values of large-seeded cultivars implies that commercial dry bean classes should be compared separately based on center of domestication.Contributions from Michigan Bean Commission, Michigan Bean Shippers Assoc. and Michigan Agric. Exp. Sta., Michigan Agric. Exp. Sta. Journal Article No. 11986     

Dynamics of genetic diversity in winter common wheat Triticum aestivum L. cultivars released in Russia from 1929 to 2005

Genealogical analysis was used to study the dynamics of genetic diversity in Russian cultivars of winter common wheat from 1929 to 2005. The Shannon diversity index of the total set of released cultivars remained almost unchanged, although the number of original ancestors (landraces and genetic lines) increased almost tenfold in the period under study. This was explained in terms of the dependence of the modified Shannon diversity index on two parameters, the number of original ancestors and the mean coefficient of parentage. Significant direct effects were revealed: a positive effect of the former parameter and a negative of the latter. As a result, the increase in the number of original ancestors was compensated by the increase in relatedness of cultivars. Genetic erosion of released diversity was observed, as a half of Russian landraces were lost. Although the mean coefficient of parentage did not reach its critical value $(\bar R = 0.25)$ , cultivars of some regions (Central and Volga-Vyatka) proved to be closely related. A favorable gradual decrease in the mean coefficient of parentage was observed in the past 15 years. A set of modern winter wheat cultivars, which were introduced in the Russian Official List from 2002 to 2005, displayed a cluster structure. The overwhelming majority of cultivars formed two clusters originating from Bezostaya 1 (67% of cultivars) and Mironovskaya 808 (31%).     

Genetic diversity and population structure among cultivars of Saccharina japonica currently farmed in northern China

Close to 50% of the annual production of the brown alga Saccharina japonica, about 2 million tons (fresh weight), is produced through farming in Shandong province, China, principally around Rongcheng. Under artificial selection for phenotypic traits (e.g. color, blade length) cultivated strains (cultivars) face the problems of inbreeding depression, which can be caused by the close relationships of the parental plants. Hence, in an attempt to evaluate genetic variations and relationships among cultivars, 15 major farmed cultivars were selected and sampled from seven major hatcheries and analyzed using 15 microsatellite markers. A total of 94 alleles were found across all samples, with allele numbers ranging from three to 17 per locus. All of the cultivars exhibited relatively high levels of genetic diversity, with mean Nei's genetic diversity (H) and the Shannon's information index (I) of 0.466 and 0.862, respectively. A UPGMA dendrogram grouped all cultivars into three main clusters. However, two of the most commonly farmed cultivars (DB and BN) from different hatcheries failed to cluster together. Instead, differently named cultivars from the same hatchery tended to group together, implying that their high similarities is partly due to the presence of genetic mixing among cultivars within a hatchery or misuse of cultivar's names. Genetic analysis performed by Bayesian model‐based clustering revealed clear differentiation of three major subgroups (LJ‐202 and LJ‐205; LJ‐C033; XS‐2 and XS‐BN) and one admixed group (the remaining ten cultivars). Our results revealed ambiguous genetic relationships among certain cultivars of S. japonica farmed in northern China. A more stringent and prudent regulation should be applied during breeding and production process in the future.     

Genetic identification of 91 poplar cultivars based on SSR markers

Accurate genetic identification and relationship analysis of poplar cultivars is necessary to establish commercial poplar plantations and select suitable breeding strategies. In this study, 91 poplar cultivars belonging to four sections (Aigeiros, Tacamahaca, Populus and Turanga) and inter/intra-sectional hybrids were genotyped using 18 polymorphic simple sequence repeat (SSR) markers. In total, 222 alleles were amplified with an average of 12.3 alleles per marker. The mean polymorphic information content and power of discrimination were 0.706 and 0.813, respectively. Five SSR markers (ORPM_103, ORPM_247, GCPM_1048, GCPM_1255 and LG_X_19) constituted a core fingerprint and were sufficient to identify all the tested cultivars. With some notable exceptions, cultivars of the same species generally clustered together in cluster (UPGMA) and ordination (PCO) analyses. Flow cytometry indicated that 11 poplar cultivars were triploid. Among these, seven had three alleles at some loci, suggesting that SSR markers could indicate the ploidy level to some extent. This study provides useful genetic information for the identification and protection of poplar cultivars in China and offers a guideline for the selection of poplar crossing parents based on ploidy level and genetic relationships.     

Dynamics of genetic diversity in winter common wheat Triticum aestivum L. cultivars released in Russia from 1929 to 2005

Genealogical analysis was used to study the dynamics of genetic diversity in Russian cultivars of winter common wheat from 1929 to 2005. The Shannon diversity index of the total set of released cultivars remained almost unchanged, although the number of original ancestors (landraces and genetic lines) increased almost tenfold in the period under study. This was explained in terms of the dependence of the modified Shannon diversity index on two parameters, the number of original ancestors and the mean coefficient of parentage. Significant direct effects were revealed: a positive effect of the former parameter and a negative of the latter. As a result, the increase in the number of original ancestors was compensated by the increase in relatedness of cultivars. Genetic erosion of realized diversity was observed, as a half of Russian landraces were lost. Although the mean coefficient of parentage did not reach its critical value (R = 0.25), cultivars of some regions (Central and Volga-Vyatka) proved to be closely related. A favorable gradual decrease in the mean coefficient of parentage was observed in the past 15 years. A set of modem winter wheat cultivars, which were introduced in the Russian State Catalog from 2002 to 2005, displayed a cluster structure. The overwhelming majority of cultivars formed two clusters originating from Bezostaya 1 (67% of cultivars) and Mironovskaya 808 (31%).     

Analysis of genetic variability in two diploid <Emphasis Type="Italic">Musa</Emphasis> cultivars using RAPD

Twenty accessions of the sparsely cultivated diploid Musa cultivars Matti (AA) and Rasakadali (AB) were subjected to random amplified polymorphic DNA (RAPD) assay. A total of 14 random primers were used for the estimation of interand intracultivar variations. Out of 86 bands generated, 64 were polymorphic (74.4 % polymorphism). The cluster analysis grouped the cultivars into two major clusters: cluster I with 10 accessions of Matti and 2 of Rasakadali and cluster II comprising the remaining 8 accessions of Rasakadali. The coefficient of genetic similarity (GS) was from 0.73 to 0.99, suggesting low level of intercultivar variation. The accessions of Rasakadali with mean GS of 0.89 were genetically more diverse than those of Matti (GS = 0.93).     

Random amplified polymorphic DNA (RAPD) analysis in Indian mung bean (Vigna radiata (L.) Wilczek) cultivars

Greengram [Vigna radiata (L.) Wilczek], also known as mung bean, widely cultivated in a large number of countries, is an important pulse crop of Asia and is considered one of the ancestral species of the genus Vigna. Since yields of greengram have remained low across subtropical and tropical Asia, it is important to estimate genetic diversity in existing cultivars in order to see if the lack of genetic variability might be a constraining factor. In this study, 32 Indian cultivars of greengram were subjected to random amplified polymorphic DNA (RAPD) analysis using 21 decamer primers. A total of 267 amplification products were formed at an average of 12.71 per primer with an overall polymorphism of 64%. The extent of polymorphism was moderate to low. Jaccard similarity coefficient values ranged from 0.65 to 0.92. The cluster analysis resulted in mainly three clusters revealing greater homology between cultivars released from the same source. The results of principal components analysis also substantiated this conclusion. The close genetic similarity between the cultivars could be explained due to the high degree of commonness in their pedigrees. The narrow genetic base of the greengram cultivars revealed in the present analysis emphasises the need to exploit the large germplasm collections having diverse morphoagronomic traits in cultivar improvement programs. This revised version was published online in July 2006 with corrections to the Cover Date.     

The use of microsatellite markers for the detection of genetic similarity among winter bread wheat lines for chromosome 3A

Previous studies with chromosome substitution and recombinant inbred chromosome lines identified that chromosome 3A of wheat cv. Wichita contains alleles that influence grain yield, yield components and agronomic performance traits relative to alleles on chromosome 3A of Cheyenne, a cultivar believed to be the founder parent of many Nebraska developed cultivars. This study was carried out to examine the genetic similarity among wheat cultivars based on the variation in chromosome 3A. Forty-eight cultivars, two promising lines and four substitution lines (in duplicate) were included in the study. Thirty-six chromosome 3A-specific and 12 group-3 barley simple sequence repeat (SSR) primer pairs were used. A total of 106 polymorphic bands were scored. Transferability of barley microsatellite markers to wheat was 73%. The coefficient of genetic distance (D) among the genotypes ranged from 0.40 to 0.91 and averaged D=0.66. Cluster analysis by the unweighted pair-group method with arithmetic averages showed one large and one small cluster with eight minor clusters in the large cluster. Several known pedigree relationships largely corresponded with the results of SSR clusters and principal coordinate analysis. Cluster analysis was also carried out by using 22 alleles that separate Wichita 3A from Cheyenne 3A, and three clusters were identified (a small cluster related to Cheyenne of mainly western Nebraska wheat cultivars; a larger, intermediate cluster with many modern Nebraska wheat cultivars; a large cluster related to Wichita with many modern high-yielding or Kansas wheat cultivars). Using three SSR markers that identify known agronomically important quantitative trait loci (QTL) regions, we again separated the cultivars into three main clusters that were related to Cheyenne or Wichita, or had a different 3A lineage. These results suggest that SSR markers linked to agronomically important QTLs are a valuable asset for estimating both genetic similarity for chromosome 3A and how the chromosome has been used in cultivar improvement.     

Assessment of Genetic Polymorphism in Hop (Humulus lupulus L.) Cultivars by ISSR–PCR Analysis

Genetic diversity among 26 Russian and European cultivars of the common hop (Humulus lupulusL.) was studied using the ISSR–PCR technique. Twenty-one primers used provided amplification of 183 DNA fragments, 106 of which (57.9%) were found to be polymorphic. The ISSR markers, specific for some cultivars were revealed. Based on the genetic distances, cluster analysis was performed and a dendrogram was constructed, on which most of the hop cultivars formed two clusters according to their origin. Advantages of the ISSR–PCR analysis in breeding studies for classification and identification of common hop cultivars are discussed.     

Assessment of Genetic Diversity of Sweet Potato in Puerto Rico

Sweet potato (Ipomoea batatas L.) is the seventh most important food crop due to its distinct advantages, such as adaptability to different environmental conditions and high nutritional value. Assessing the genetic diversity of this important crop is necessary due to the constant increase of demand for food and the need for conservation of agricultural and genetic resources. In Puerto Rico (PR), the genetic diversity of sweet potato has been poorly understood, although it has been part of the diet since Pre-Columbus time. Thus, 137 landraces from different localities around PR were collected and subjected to a genetic diversity analysis using 23 SSR-markers. In addition, 8 accessions from a collection grown in Gurabo, PR at the Agricultural Experimental Station (GAES), 10 US commercial cultivars and 12 Puerto Rican accessions from the USDA repository collection were included in this assessment. The results of the analysis of the 23 loci showed 255 alleles in the 167 samples. Observed heterozygosity was high across populations (0.71) while measurements of total heterozygosity revealed a large genetic diversity throughout the population and within populations. UPGMA clustering method revealed two main clusters. Cluster 1 contained 12 PR accessions from the USDA repository collection, while cluster 2 consisted of PR landraces, US commercial cultivars and the PR accessions from GAES. Population structure analysis grouped PR landraces in five groups including four US commercial cultivars. Our study shows the presence of a high level of genetic diversity of sweet potato across PR which can be related to the genetic makeup of sweet potato, human intervention and out-crossing nature of the plant. The history of domestication and dispersal of sweet potato in the Caribbean and the high levels of genetic diversity found through this study makes sweet potato an invaluable resource that needs to be protected and further studied.     

The population genomic signature of environmental association and gene flow in an ecologically divergent tree species Metrosideros polymorpha (Myrtaceae)

Genomewide markers enable us to study genetic differentiation within a species and the factors underlying it at a much higher resolution than before, which advances our understanding of adaptation in organisms. We investigated genomic divergence in Metrosideros polymorpha, a woody species that occupies a wide range of ecological habitats across the Hawaiian Islands and shows remarkable phenotypic variation. Using 1659 single nucleotide polymorphism (SNP) markers annotated with the genome assembly, we examined the population genetic structure and demographic history of nine populations across five elevations and two ages of substrates on Mauna Loa, the island of Hawaii. The nine populations were differentiated into two genetic clusters distributed on the lower and higher elevations and were largely admixed on the middle elevation. Demographic modelling revealed that the two genetic clusters have been maintained in the face of gene flow, and the effective population size of the high‐altitude cluster was much smaller. A F_ST‐based outlier search among the 1659 SNPs revealed that 34 SNPs (2.05%) were likely to be under divergent selection and the allele frequencies of 21 of them were associated with environmental changes along elevations, such as temperature and precipitation. This study shows a genomic mosaic of M. polymorpha, in which contrasting divergence patterns were found. While most genomic polymorphisms were shared among populations, a small fraction of the genome was significantly differentiated between populations in diverse environments and could be responsible for the dramatic adaptation to a wide range of environments.     

Characterization of <Emphasis Type="Italic">Brassica napus</Emphasis> L. genotypes utilizing sequence-related amplified polymorphism and genotyping by sequencing in association with cluster analysis

Identifying parental combinations that exhibit high heterosis is a constant target for commercial Brassica napus L. hybrid development programs. Finding high heterotic parental combinations can require hundreds of test crosses and years of yield evaluation. Heterotic pool development could be used to divide breeding material into specific breeding pools and focus the number of parental combinations created. Here, we report the genotypic characterization of 79 B. napus genotypes by calculating genetic distance based on sequence-related amplified polymorphism (SRAP) and genotyping by sequencing (GBS) in association with a neighbour-joining clustering algorithm. Despite the different genotypic analyses, neighbour-joining cluster analysis based on genetic distance of SRAP and GBS produced similar clusters. Homology between SRAP and GBS clusters was approximately 77 % when manually comparing clusters and 68 % when comparing clusters using Compare2Trees. This research demonstrates that SRAP can have similar efficacy when compared to next-generation sequencing technology for heterotic pool classification. This information may provide an important breeding scaffold for the development of hybrid cultivars based upon genetic distance and cluster analysis.     

Molecular diversity and relationships among <Emphasis Type="Italic">Cymbidium goeringii</Emphasis> cultivars based on inter-simple sequence repeat (ISSR) markers

Spring orchid (Cymbidium goeringii) is a popular flowering plant species. There have been few molecular studies of the genetic diversity and conservation genetics on this species. An assessment of the level of genetic diversity in cultivated spring orchid would facilitate development of the future germplasm conservation for cultivar improvement. In the present study, DNA markers of intersimple sequence repeats (ISSR) were identified and the ISSR fingerprinting technique was used to evaluate genetic diversity in C. goeringii cultivars. Twenty-five ISSR primers were selected to produce a total of 224 ISSR loci for evaluation of the genetic diversity. A wide genetic variation was found in the 50 tested cultivars with Nei’s gene diversity (H = 0.2241) and 93.75% of polymorphic loci. Fifty cultivars were unequivocally distinguished based on ISSR fingerprinting. Cultivar-specific ISSR markers were identified in seven of 50 tested cultivars. Unweighted pair-group mean analysis (UPGMA) and principal coordinates analysis (PCA) grouped them into two clusters: one composed the cultivars mainly from Japan, and the other contained three major subclusters mainly from China. Two Chinese subclusters were generally consistent with horticultural classification, and the third Chinese subcluster contained cultivars from various horticultural groups. Our results suggest that the ISSR technique provides a powerful tool for cultivar identification and establishment of genetic relationships of cultivars in C. goeringii.     

Identification and analysis of genetic variation among rose cultivars using random amplified polymorphic DNA

Identified germplasm is an important component for efficient and effective management of plant genetic resources. Traditionally, cultivars or species identification has relied on morphological characters like growth habit or floral morphology like flower colour and other characteristics of the plant. Studies were undertaken for identification and analysis of genetic variation within 34 rose cultivars through random amplified polymorphic DNA (RAPD) markers. Analysis was made by using twenty five decamer primers. Out of twenty five, ten primers were selected and used for identification and analysis of genetic relationships among 34 rose cultivars. A total of 162 distinct DNA fragments ranging from 0.1 to 3.4 kb was amplified by using 10 selected random decamer primers. The genetic similarity was evaluated on the basis of presence or absence of bands. The cluster analysis indicated that the 34 rose cultivars form 9 clusters. The first cluster consists of eight hybrid cultivars, three clusters having five cultivars each, one cluster having four cultivars, two clusters having three cultivars each and two clusters having one cultivar each. The genetic distance was very close within the cultivars. Thus, these RAPD markers have the potential for identification of clusters and characterization of genetic variation within the cultivars. This is also helpful in rose breeding programs and provides a major input into conservation biology.     

Genetic Diversity and Population Structure Among Oat Cultivars and Landraces

In this study, genetic diversity among 177 oat (Avena sativa L.) accessions including both white and red oat landraces and 36 commercial cultivars was studied for simple sequence repeat (SSR) loci. Thirty-one genomic and expressed sequence tags (EST)-derived primer pairs were selected according to high polymorphism from an initial 66 SSR batch. Markers revealed a high level of polymorphism, detecting a total of 454 alleles. The average gene diversity for the whole sample was 0.29. Genetic similarity, calculated using the Dice coefficient, was used for cluster analysis, and principal component analysis was also applied. In addition, population structure using a Bayesian clustering approach identified discrete subpopulation based on allele frequency and showed similar clustering of oat genotypes in four groups. Accessions could be classified into four main clusters that clearly separated the commercial cultivars, the red oat landraces and two clusters of white oat landraces. Cultivars showed less diversity than the landraces indicating a reduction of genetic diversity during breeding, whereas white oat landraces showed higher diversity than red ones. The average polymorphic information content of 0.80 for the SSR loci indicated the usefulness of many of the SSR for genotype identification. In particular, two markers, MAMA5 and AM04, with a total of 50 alleles and a high discrimination power (>0.90), were sufficient to discriminate among all commercial cultivars studied highlighting their potential use for variety identification.     

An approach for identifying cryptic barriers to gene flow that limit species' geographic ranges

Species' geographic range limits are most often not demarcated by obvious dispersal barriers. Poor‐quality habitat at the edge of a species' range can prevent range expansion by preventing outward migration or through reducing adaptive potential resulting from decreased genetic diversity. We identified habitat variables that constrain gene flow across the entire geographic range of an endemic salamander (Ambystoma barbouri) in the eastern United States, and we tested whether increased resistance resulting from these variables provides cryptic dispersal barriers at the range edges. Using polymorphic microsatellite loci, we first identified three genetic clusters that are separated by the Ohio and Kentucky rivers. Through a combination of landscape genetic analyses and generalized dissimilarity modelling, we then classified variables that (i) restrict gene flow in each of the genetic clusters across the geographic distribution of A. barbouri and (ii) become more common towards the peripheries of the distribution. A decrease in limestone availability and an increase in growing season precipitation were correlated with high resistance to gene flow across the range, and both became more common at the edges of the species' distribution. However, other landscape variables were more important for explaining variation in geneflow rates in different portions of the range, such as increased mean annual temperature and frost‐free period in the south vs. growing season precipitation in the north. Taken together, these results suggest that there are both range‐wide and regionally specific cryptic habitat barriers preventing geographic range expansion. Species ‘geographic range limits are probably governed by a set of ecological and evolutionary factors, and our landscape genetic approach could be applied to gain additional insight into many systems.     

Relationship between genetic distance and heterosis for yield and morphological traits in winter canola (Brassica napus L.)

Genetic distance among canola cultivars was estimated through multivariate analysis. Thirty cultivars from various sources were analyzed and clustered based upon five morphological characteristics and yield components-crown diameter, number of branches plant^-1, number of pods plant^-1, number of seeds pod^-1 and yield plant^-1 -and placed in three distinct clusters. Two cultivars from each cluster were selected as parents and 15 partial-diallel inter- and intra-cluster crosses were made between the six selected parents and evaluated at two locations in Michigan in 1990/1991. The association between genetic distance and mid-parent heterosis was investigated. The correlation between genetic distance and heterosis was positive and highly significant for seed yield, number of pods plant^-1, and number of seeds pod^-1. Clustering, based on yield and yield-component traits, demonstrated that inter-cluster heterosis was greater than intra-cluster heterosis in the majority of cases.     

QTL analysis of frost damage in pea suggests different mechanisms involved in frost tolerance

Key message

Avoidance mechanisms and intrinsic resistance are complementary strategies to improve winter frost tolerance and yield potential in field pea.

Abstract

The development of the winter pea crop represents a major challenge to expand plant protein production in temperate areas. Breeding winter cultivars requires the combination of freezing tolerance as well as high seed productivity and quality. In this context, we investigated the genetic determinism of winter frost tolerance and assessed its genetic relationship with yield and developmental traits. Using a newly identified source of frost resistance, we developed a population of recombinant inbred lines and evaluated it in six environments in Dijon and Clermont-Ferrand between 2005 and 2010. We developed a genetic map comprising 679 markers distributed over seven linkage groups and covering 947.1 cM. One hundred sixty-one quantitative trait loci (QTL) explaining 9–71 % of the phenotypic variation were detected across the six environments for all traits measured. Two clusters of QTL mapped on the linkage groups III and one cluster on LGVI reveal the genetic links between phenology, morphology, yield-related traits and frost tolerance in winter pea. QTL clusters on LGIII highlighted major developmental gene loci (Hr and Le) and the QTL cluster on LGVI explained up to 71 % of the winter frost damage variation. This suggests that a specific architecture and flowering ideotype defines frost tolerance in winter pea. However, two consistent frost tolerance QTL on LGV were independent of phenology and morphology traits, showing that different protective mechanisms are involved in frost tolerance. Finally, these results suggest that frost tolerance can be bred independently to seed productivity and quality.     

Use of artificial environments to reproduce and exploit genotype × location interaction for lucerne in northern Italy

Genotype × environment interaction effects can be exploited by breeding for specific adaptation to well-defined subregions within a target region. Previous work showed that genotype × location interaction for dry matter (DM) yield of lucerne (Medicago sativa L. subsp. sativa) cultivars in northern Italy is large and associated with soil type and level of summer drought stress of locations, suggesting the presence of two contrasting subregions. Thirteen farm landraces collected across the region and four control varieties were evaluated for DM yield in four artificial environments created at one site by the factorial combination of soil type (sandy loam or silty clay) and drought stress level (almost nil or high) for: (1) exploring the possibility to reproduce in artificial environments the adaptation patterns occurring across the region; (2) investigating the adaptation pattern of landraces and its relationship with environmental factors at collecting sites; and (3) providing a preliminary comparison of wide- versus specific-adaptation strategies based on yield gains predicted from selection of populations. Different soils filled large (24.0×1.6×0.8-m deep), bottomless containers in concrete. Water amounts were controlled by irrigation under a moving rain shelter. Cultivars varied largely for adaptation pattern across the artificial environments, mainly due to cultivar × stress interaction. Better response to stress conditions of landraces was closely associated with the level of summer drought at collecting sites (r=0.82), highlighting the importance of evolutionary adaptation. The additive main effects and multiplicative interaction-modelled responses of control cultivars successfully reproduced those observed across locations, candidating the artificial environments as a cheaper alternative to more selection locations when breeding for wide or specific adaptation. The latter implied about 40–50% greater estimated gains relative to breeding for wide adaptation.