Knowledge about germplasm diversity and genetic relationships among breeding materials could be an invaluable aid in crop improvement strategies. A number of methods are currently available for analysis of genetic diversity in germplasm accessions, breeding lines, and populations. These methods have relied on pedigree data, morphological data, agronomic performance data, biochemical data, and more recently molecular (DNA-based) data. For reasonably accurate and unbiased estimates of genetic diversity, adequate attention has to be devoted to (i) sampling strategies; (ii) utilization of various data sets on the basis of the understanding of their strengths and constraints; (iii) choice of genetic distance measure(s), clustering procedures, and other multivariate methods in analyses of data; and (iv) objective determination of genetic relationships. Judicious combination and utilization of statistical tools and techniques, such as bootstrapping, is vital for addressing complex issues related to data analysis and interpretation of results from different types of data sets, particularly through clustering procedures. This review focuses on application of statistical tools and techniques in analysis of genetic diversity at the intraspecific level in crop plants.

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Analysis of Genetic Diversity in Crop Plants—Salient Statistical Tools and Considerations

A proper choice of a dissimilarity measure is important in surveys investigating genetic relationships among germplasm with molecular marker data. The objective of our study was to examine 10 dissimilarity coefficients widely used in germplasm surveys, with special focus on applications in plant breeding and seed banks. In particular, we (i) investigated the genetical and mathematical properties of these coefficients, (ii) examined consequences of these properties for different areas of application in plant breeding and seed banks, and (iii) determined relationships between these 10 coefficients. The genetical and mathematical concepts of the coefficients were described in detail. A Procrustes analysis of a published data set consisting of seven CIMMYT maize populations demonstrated close affinity between Euclidean, Rogers', modified Rogers', and Cavalli-Sforza and Edwards' distance on one hand, and Nei's standard and Reynolds dissimilarity on the other hand. Our investigations show that genetical and mathematical properties of dissimilarity measures are of crucial importance when choosing a genetic dissimilarity coefficient for analyzing molecular marker data. The presented results assist experimenters to extract the maximum amount of information from genetic data and, thus, facilitate the interpretation of findings from molecular marker studies on a theoretically sound basis.

Genetical and Mathematical Properties of Similarity and Dissimilarity Coefficients Applied in Plant Breeding and Seed Bank Management

It is the purpose of this paper to illustrate the impact of geography, climate, and humankind in shaping the present-day genetic diversity in soybean [Glycine max (L.) Merr.]. Examination of soybean germplasm collections around the globe reveals that an enormous phenotypic range in genetic traits exists in soybean, which is well beyond the phenotypic range observed in the wild progenitor (Glycine soja Seib. et Zucc.). Maturity date, seed coat color, plant height, seed size, and seed yield are noted examples of traits which have a wider phenotypic range in G. max than in the wild G. soja. The diversity found in domesticated soybean is the result of over 3,000 years of cultivation in which Chinese farmers selected more than 20,000 landraces ( defmed as cultivars that predate scientific breeding). The extensive range in phenotype embodied in landraces today is the result of the slow spread of soybean throughout geographically diverse Asia (China first, then Korea and Japan), the continual occurrence of natural mutations in the crop, and both conscious and unconscious selection for local adaptation. The more recent spread of soybean out of Asia in the past 250 years, coupled with modem breeding efforts of the past 70, has intensified and globalized the process of local adaptation and increased the phenotypic range in soybean beyond that of landraces. The increased range in phenotype for modem cultivars includes increases in seed yield, elevation of seed protein/oil concentration, and development, only within the past 20 years, of commercial cultivars that are sufficiently tall and adapted to be grown profitably near the equator. The phenotypic range and distribution observed in modem cultivars and antecedent landraces have clear biogeographical interpretations which relate primarily to genetic alteration of photoperiod response (a prerequisite to adaptation to diverse latitudes) and tolerance to climate extremes. Although the phenotypic range in genetic traits has been expanded in modem soybean through global dispersal and genetic recombination, it is perhaps surprising that that these factors have not had a corresponding positive impact on genetic diversity of modem breeding programs outide of China.. Genetic diveresity in breeding programs is important as a concept, because it is a measure of the potential of a country to develop new and substantially improved cultivars. For the purposes of this paper, genetic diversity in breeding programs is defined, as ge-

Genetic Diversity in Soybean

Random amplified polymorphic DNA, simple sequence repeat, and inter-simple sequence repeat markers were used to estimate the genetic relations among 65 pea varieties (Pisum sativum L.) and 21 accessions from wild Pisum subspecies (subsp.) abyssinicum, asiaticum, elatius, transcaucasicum, and var. arvense. Fifty-one of these varieties are currently available for growers in western Canada. Nei and Li's genetic similarity (GS) estimates calculated using the marker data showed that pair-wise comparison values among the 65 varieties ranged from 0.34 to 1.00. GS analysis on varieties grouped according to their originating breeding programs demonstrated that different levels of diversity were maintained at different breeding programs. Unweighted pair-group method arithmetic average cluster analysis and principal coordinate analysis on the marker-based GS grouped the cultivated varieties separately from the wild accessions. The majority of the food and feed varieties were grouped separately from the silage and sp...

Genetic diversity among varieties and wild species accessions of pea (Pisum sativum L.) based on molecular markers, and morphological and physiological characters.

AFLP markers were used to assess the genetic diversity of 77 breeding lines from three of the world's major canola qualityBrassica juncea breeding programs from Canada (Agriculture and Agri-Food Canada and Saskatchewan Wheat Pool) and Australia (Agriculture Victoria). The objectives of the paper were to assess the genetic diversity within and between these three breeding programs and to assess genetic diversity of the canola quality germplasm as compared to mustard quality B. juncea. Fifteen lines of mustard quality B. juncea from India, China, Russia and Australia were also included in the investigation. Ten EcoR1/Mse1 based primer pairs generated 751 scorable fragments with an average of 26 polymorphic bands per primer pair (35%). Similarity coefficients were calculated using the Simple Matching coefficient and adendrogram was developed using the UPGMA procedure, resulting in germplasm being partitioned into five main groups. Line specific markers were discovered that have potential in enhancing the efficiency of individual breeding programs using breeding techniques like accelerated backcrossing. Further understanding the genetic diversity within and between programs has implications for future breeding and collaboration within and between the three programs.

Assessment of genetic diversity in selected breeding lines and cultivars of canola quality Brassica juncea and their implications for canola breeding

At present, registration and protection of rapeseed (Brassica napus L) cultivars relies on a small number of morphological traits, As the number of cultivars increases, the ability to distinguish them on the basis of these traits becomes more difficult New descriptors like molecular markers are required to maintain the efficiency of registration testing The objectives of this study were to (i) evaluate the discrimination power of 17 amplified fragment length polymorphism (AFLP) primer combinations tested on a collection of 83 spring and winter rapeseed cultivars, (ii) assess the structure of the genetic diversity revealed by AFLPs, and (iii) compare three genetic distance estimators (Jaccard, Sokal, and Michener and Sokal and Michener weighted by the PIC) A total of 324 polymorphic markers were scored, with an average of 191 markers per primer combination The use of only two primer combinations was sufficient to identify uniquely all the cultivars The analysis of the genetic structure of the diversity by cluster and principal component analyses and AMOVAs (analyses of molecular variance) clearly delineated three significant factors: the cultivar type (winter or spring) the country of origin (France or Germany), and the breeding company The three measures of genetic distance were highly correlated (P < 0001, r = 096-098) and led to similar groupings AFLPs were shown to be a powerful method for identifying cultivars and analyzing the genetic structure of the diversity in rapeseed

Genetic Relationships and Fingerprinting of Rapeseed Cultivars by AFLP: Consequences for Varietal Registration

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Genetic Relationships and Fingerprinting of Rapeseed Cultivars by AFLP: Consequences for Varietal Registration