Genetic Diversity Of Cultivars Research Articles

Phylogeography of cultivated and wild ophiopogon japonicus based on chloroplast DNA: exploration of the origin and sustainable cultivation

BackgroundOphiopogon japonicus, mainly planted in Sichuan (CMD) and Zhejiang (ZMD) province in China, has a lengthy cultivation history. During the long period of domestication, the genetic diversity of cultivated O. japonicus has substantially declined, which will affect the population continuity and evolutionary potential of this species. Therefore, it is necessary to clarify the phylogeography of cultivated O. japonicus to establish a theoretical basis for the utilization and conservation of the genetic resources of O. japonicus.ResultThe genetic diversity and population structure of 266 O. japonicus individual plants from 23 sampling sites were analyzed based on 4 chloroplast DNA sequences (atpB-rbcL, rpl16, psbA-trnH and rpl20-5’rps12) to identify the effects of domestication on genetic diversity of cultivars and determine their geographic origins. The results showed that cultivated O. japonicus and wild O. japonicus had 4 and 15 haplotypes respectively. The genetic diversity of two cultivars (Hd = 0.35700, π = 0.06667) was much lower than that of the wild populations (Hd = 0.76200, π = 0.20378), and the level of genetic diversity in CMD (Hd = 0.01900, π = 0.00125) was lower than that in ZMD (Hd = 0.06900, π = 0.01096). There was significant difference in genetic differentiation between the cultivated and the wild (FST = 0.82044), especially between the two cultivars (FST = 0.98254). This species showed a pronounced phylogeographical structure (NST > GST, P < 0.05). The phylogenetic tree showed that the genetic difference between CMD and ZMD was not enough to distinguish the cultivars between the two producing areas by using O. amblyphyllus Wang et Dai as an outgroup. In addition, both CMD and ZMD have a closer relationship with wild populations in Sichuan than that in Zhejiang. The results of the TCS network and species distribution model suggested that the wild population TQ located in Sichuan province could serve as the ancestor of cultivated O. japonicus, which was supported by RASP analysis.ConclusionThese results suggest that cultivated O. japonicus has experienced dramatic loss of genetic diversity under anthropogenic influence. The genetic differentiation between CMD and ZMD is likely to be influenced by founder effect and strong artificial selection for plant traits. It appears that wild populations in Sichuan area are involved in the origin of not only CMD but also ZMD. In addition, we also raise some suggestions for planning scientific strategies for resource conservation of O. japonicus based on its genetic diversity and population structure.

Investigation on genetic diversity of pepper (Capsicum spp.) parents and interspecific hybrids using ISSR markers

Pepper (Capsicum) is one of the most important and widespread vegetable crops in the Balkans. Some old indigenous forms are not the focus of modern breeding but are preserved in some areas and represent valuable genetic resources. Three Bulgarian varieties (Plovdivska kapiya, Familiya and IZK Delicates) C. annuum, and two representatives of the chili pepper C. chinense and C. frutescens. Interspecific hybrids were made between sweet (C. annum) and chili pepper plants. The genetic relationships of the varieties of Capsicum species were assessed using ISSR primers. PCR amplification of isolated DNA from parental lines and interspecific hybrids revealed 65 distinct polymorphic bands. Cluster analysis clearly distinguished the parental forms and individuals from the F1 and F2 populations. The applied ISSR molecular technique can be successfully used to analyze genetic diversity in cultivars, early-stage seedlings, and interspecific hybrids, as well as to detect differences in individuals whose genomes are highly homogeneous, such as those of the genus Capsicum.

Kelps in Korea: from population structure to aquaculture to potential carbon sequestration

Korea is one of the most advanced countries in kelp aquaculture. The brown algae, Undaria pinnatifida and Saccharina japonica are major aquaculture species and have been principally utilized for human food and abalone feed in Korea. This review discusses the diversity, population structure and genomics of kelps. In addition, we have introduced new cultivar development efforts considering climate change, and potential carbon sequestration of kelp aquaculture in Korea. U. pinnatifida showed high diversity within the natural populations but reduced genetic diversity in cultivars. However, very few studies of S. japonica have been conducted in terms of population structure. Since studies on cultivar development began in early 2000s, five U. pinnatifida and one S. japonica varieties have been registered to the International Union for the Protection of New Varieties of Plants (UPOV). To meet the demands for seaweed biomass in various industries, more cultivars should be developed with specific traits to meet application demands. Additionally, cultivation technologies should be diversified, such as integrated multi-trophic aquaculture (IMTA) and offshore aquaculture, to achieve environmental and economic sustainability. These kelps are anticipated to be important sources of blue carbon in Korea.

Profiling the Diversity of Sweet Pepper ‘Peperone Cornetto di Pontecorvo’ PDO (Capsicum annuum) through Multi-Phenomic Approaches and Sequencing-Based Genotyping

The sweet pepper (Capsicum annuum) ‘Peperone Cornetto di Pontecorvo’ is a prominent local variety at risk of genetic erosion cultivated in the Latium region (Italy). This horn-shaped landrace is recognized for its high digestibility due to the thinness of the skin and has been granted the Protected Designation of Origin (PDO) mark since 2010. Nowadays, different accessions are claimed as ‘Peperone Cornetto di Pontecorvo’ and no assay has been conducted to determine authenticity. In this study, 14 ‘Peperone Cornetto di Pontecorvo’ accessions and 7 similar horn-type peppers were investigated for their morpho-agronomic performance and chemical composition. Digital fruit imaging was implemented as a tool to pinpoint with high accuracy the morphometric parameters of berries. In total, 52 traits were scored. The multivariate analysis revealed different clusters that separated ‘Peperone Cornetto di Pontecorvo’ from similar types. The weight and size of fruits, as well as the content of soluble solids, were the most discriminating factors among the cultivars studied. Genomic fingerprinting was performed using ddRAD sequencing, yielding a total of a total of 120 million raw sequences and 2196 high-quality SNPs. Both Bayesian and hierarchical clustering analyses confirmed the existence of two different (K = 2) sub-populations separating ‘Peperone Cornetto di Pontecorvo’ accessions from similar types, thus highlighting a high membership (qi &gt; 0.97) coefficient for accessions cultivated in the Pontecorvo area (Frosinone district). In addition, a direct relationship was found between the genetic diversity of cultivars and their geographical provenance, providing hints on the breeding history of local varieties in diverse rural areas. Genomic markers are revealed as a valuable tool to establish the uniqueness and distinctness of this local variety. This information will be very helpful for recovery, enhancement, and protection from possible imitations.

Putative variants, genetic diversity and population structure among Soybean cultivars bred at different ages in Huang-Huai-Hai region

Soybean cultivars bred in the Huang-Huai-Hai region (HR) are rich in pedigree information. To date, few reports have exposed the genetic variants, population structure and genetic diversity of cultivars in this region by making use of genome-wide resequencing data. To depict genetic variation, population structure and composition characteristics of genetic diversity, a sample of soybean population composed all by cultivars was constructed. We re-sequenced 181 soybean cultivar genomes with an average depth of 10.38×. In total, 11,185,589 single nucleotide polymorphisms (SNPs) and 2,520,208 insertion-deletions (InDels) were identified on all 20 chromosomes. A considerable number of putative variants existed in important genome regions that may have an incalculable influence on genes, which participated in momentous biological processes. All 181 varieties were divided into five subpopulations according to their breeding years, SA (1963–1980), SB (1983–1988), SC (1991–2000), SD (2001–2011), SE (2012–2017). PCA and population structure figured out that there was no obvious grouping trend. The LD semi-decay distances of sub-population D and E were 182 kb, and 227 kb, respectively. Sub-population A (SA) had the highest value of nucleotide polymorphism (π). With the passage of time, the nucleotide polymorphism of SB and SC decreased gradually, however that of SD and SE, opposite to SB and SC, gave a rapid up-climbing trend, which meant a sharp increase in genetic diversity during the latest 20 years, hinting that breeders may have different breeding goals in different breeding periods in HR. Analysis of the PIC statistics exhibited very similar results with π. The current study is to analyze the genetic variants and characterize the structure and genetic diversity of soybean cultivars bred in different decades in HR, and to provide a theoretical reference for other identical studies.

Wind lodging-associated yield loss is reduced by wheat genetic diversity

There is abundant evidence that biodiversity can promote crop yield by different mechanisms. However, few studies have examined trade-offs between wind lodging resistance and yield in the context of genetic diversity. Globally, wheat production practices face substantial challenges with regard to reducing yield loss due to wind lodging. Here, we conducted a field experiment in the North China Plain, and aimed to test this effect based on individual cultivars (8× monocultures) and combinations of cultivar mixtures that contained two (mixture-2), four (mixture-4), and eight (mixture-8) wheat cultivars. The results showed that there were positive relationships between grain yield and cultivar genetic diversity in patterns of mixed cultivars, which had positive impacts on wind speed, wind lodging stress in different directions, and lodging occurrence compared with their component lodging-susceptible cultivars. No wind lodging happened in mixed patterns, whereas some cultivars of monoculture lost parts of their yields due to wind lodging. Among all patterns, mixture-4 and mixture-8 had the greater wind lodging resistance than lodging-susceptible cultivars. From 2018–2020, yields of the cultivar mixture-8 was higher than those of the monocultures, although yield varied by year. In 2019, the grain yields of mixture-4 and mixture-8 increased by 3.16% and 5.84%, respectively, compared with LY502, which is the highest yielding local winter wheat cultivar. Furthermore, the yield stability is improved with increasing number of cultivar mixtures. These findings revealed that enhanced genotypic diversity of wheat population may ecologically reduce wind lodging, which can make a certain contribution to yield and its stability in intensive cropping systems.

Molecular markers : An uprising tool for crop improvement

Molecular marker is a DNA sequence in the genome of any organism which can be located and identified. Plant breeders always prefer to remark the gene as the molecular marker, although this is not always possible. A molecular marker is nothing but a small region of DNA that shows sequence polymorphism in different individuals within a species or different species. The utility of molecular marker is based on naturally occurring DNA polymorphism and its growth in utility has greatly modified genetics and plant breeding. The DNA markers are most widely used in plant breeding programmes such as in the assessment of genetic variations within cultivars, gene mapping, transferring desirable genes for biotic and abiotic resistance. Marker-assisted selection (MAS) proves to be the most fascinating approach of molecular markers. An ideal DNA marker should be polymorphic in nature and it can be expressed in all tissues, organs, at various developmental stages. When comparing between conventional breeding approaches and molecular markers, the efficiency and effectiveness of breeding programs can be increased by molecular markers. Due to the presence of different types of molecular markers, and the variation in their principles, methodologies and mode of application, they require careful consideration in selecting one or more of such methods. With advancement in the availability of types of molecular markers, they can be used for the assessment of genetic diversity in cultivars, germplasm collection and advanced breeding material, identification of homokaryonand hybrid selection. This review article attempts to consider the current resources and novel examples where the MMs have been developed and used for the improvement of cereal crops for agronomic, food quality, disease resistance, abiotic stress tolerance traits and cytogenetic studies.

Molecular and morphological characterization of Musa spp. (Zingiberales : Musaceae) cultivars.

Objectives: The overall goal was to analyze genetic diversity in cultivars of Musa acuminata (Colla) and M. balbisiana (Colla), commonly grown in farms from Caldas department. Scope: Characterization of the genetic variability, at the molecular and morphological level of cultivars of M. acuminata and M. balbisiana, found in farms from Caldas farmers using morphological descriptors and fluorescent microsatellites. Methodology: Phenotyping evaluations comprised 57 morphological characters following the descriptors proposed by IPGRI for the Musa genus, and for genotyping evaluations, nine fluorescent microsatellites (Simple Sequence Repeats-SSR) were used to allow the precise identification of alleles. Additionally, cluster analyses were carried out independently for both morphological and genotypic characterizations under Principal Component Analysis (PCA) and Bootstrapping methods respectively. Main results: Positive and negative highly significant correlations were found for the morphological descriptors, where traits such as presence/ absence of male bud was the rule, as well as the diameter and perimeter of this trait, plus the diameter and perimeter of the peduncle, number of fruits, pseudostem height and fruit length contributed considerably to the variability among the cultivars allowing the discrimination of three main groups in the cluster analyzes. From the molecular perspective a total of 72 polymorphic alleles were obtained, with an average genetic diversity of 0,79, polymorphic information content (PIC) of 0,77 and heterozygosity of 0,48, showed a moderate degree of genetic differentiation (FST = 0,061) among Musa cultivars, generating three main sub-clusters based on their genetic dissimilarity. Conclusions: The identification of certain morphological traits showed to be suitable for the discrimination of Musa cultivars evaluated here. On the other hand, molecular characterization allowed to establish the genetic relationships among groups, also fluorescent SSR were highly informative and accurate, in such a way that can be considered suitable for characterizations in Musa varieties.

Genetic Consequences of Interspecific Hybridization, Its Role in Speciation and Phenotypic Diversity of Plants

The review focuses on the genetic consequences of interspecific hybridization and discusses its role in speciation and increasing the genetic diversity of plants, including the diversity of species and varieties of cultivated crops and garden plants. The combination of two or more genomes of different origin in the first-generation hybrids is usually accompanied by a phenomenon referred to as genomic shock, which results in different genetic and epigenetic changes. As a result, a material appears which is unique in providing multiple variants for natural selection of organisms, in different degrees adapted to new environmental conditions. In isolated plant populations with various destabilized genomes of hybrid origin under the influence of natural selection and due to genetic drift, gene and chromosomal differences will accumulate, triggering new reproductive isolating mechanisms that increase genetic isolation of a new race or species. Progressive establishment of genome stabilization at the eupolyploid stage and subsequent repeated genome and karyotype diploidization facilitate the retention of selected new genomic and epigenomic combinations. It seems likely that the evolutionary history of all agricultural crops and garden plant varieties, as well as of many invasive alien species and the components of adventive flora, was marked by interspecific crossings purposefully carried out by breeders during the creation of modern varieties and crossings between previously geographically isolated plants that were unintentionally united in apothecary and botanical gardens, in fields and backyards, and on disturbed lands around settlements. At the same time, phenotypic and genetic diversity of cultivars not only results from the combination of different alleles that already existed in the genomes of the parental species but also is a consequence of the appearance in the first-generation hybrids of new genomic and epigenomic variants that are direct or distant effects of post-hybridization genomic shock, the creative role of which we would like to emphasize.

Trait collection of rice by cold tolerance

Goal. To assess rice cultivars for cold tolerance; to select the most valuable in terms of economic characteristics sources for their further use in breeding; to create a trait collection on their basis.Result and Discussion. The article presents the results of studying a rice collection. The collection material is represented by 51 accessions of different eco-geographical origin (European, Eastern, Mid-Asian, Latin American). The accessions belong to two subspecies: japonica and indica. Most of the accessions (22) are from Ukraine and account for 43.1%. Temperature is one of the most important environmental factors affecting the crop establishment and development. In Ukraine, rice is cultivated in the most northern zone of rice growing and, therefore, it is liable to negative effects of cold weather during the seed germination, sprouting, anthesis and grain ripening. Consequently, it is essential for breeders to create cultivars that will be tolerant to low temperatures during the sprouting period, with high field germinability and increased germinative power. Seed germination is particularly affected by temperature. Fifty one rice cultivars were investigated for the seedling development, seed germination rate and seedling growth intensity at 14°C; possible states of embryonic roots were estimated; lengths of these stages were determined. Selection of material with a set of parameters allowed forming a trait collection with increased levels of resistance to abiotic environmental factors. In breeding, it is very important to identify sources of valuable traits and to assess extent of their influence on the plant performance. The research distinguished rice accessions for breeding by levels of cold tolerance, performance and its components. We selected six donors of several valuable traits, the use of which will enhance the breeding efficiency (Kuban 3, Vikont, UkrNDS 8839, Ontario, VNIIR 546, Kaz ER – 6). Thus, the comprehensive assessment of the accessions allowed us not only to replenish the rice gene pool, but also, basing on this research, to choose starting material to involve it in further breeding for creating new cold-tolerant varieties. While creating such cultivars, we revealed morphological traits of rice, which are used as test parameters characterizing the stress tolerance of accessions.Conclusions. The study resulted in formation of the trait collection representing the genetic diversity of cultivars and breeding lines. Each trait and gradation has corresponding standards. Cultivars-standards reflect more specific and stable expression of a trait. The collection was created by 4 basic traits and 3 gradations and contains accessions from 9 countries (Ukraine, Russia, Kazakhstan, Uzbekistan, Kyrgyzstan, USA, Bulgaria, China, and Hungary). The standard accessions selected can serve as sources of economically valuable features to create starting material for breeding.

Genetic Diversity Analysis of Medicinally Important Horticultural Crop Aegle marmelos by ISSR Markers.

Inter simple sequence repeat (ISSR) markers help in identifying and determining the extent of genetic diversity in cultivars. Here, we describe their application in determining the genetic diversity of bael (Aegle marmelos Corr.). Universal ISSR primers are selected and their marker characteristics such as polymorphism information content, effective multiplex ratio and marker index have been evaluated. ISSR-PCR is then performed using universal ISSR primers to generate polymorphic bands. This information is used to determine the degree of genetic similarity among the bael varieties/accessions by cluster analysis using unweighted pair-group method with arithmetic averages (UPGMA). This technology is valuable for biodiversity conservation and for making an efficient choice of parents in breeding programs.

Development of an Efficient In Vitro Screening Method for Selection of Resistant Lily Cultivars Against Fusarium oxysporum f. sp. lilii

토양 전염균인 Fusarium oxysporum f. sp. lilii(Fol)은 식물에 심각한 위협을 주는 균으로 특히 백합의 구근과 꽃에 심각한 영향을 준다. 따라서 저항성 품종의 육성이 중요시되고 있는데, 저항성 품종이 육성되기 위해서는 신속, 간편한 검정법 체계와 유전적 다양성이 요구되는 상황이다. 본 실험에서는 기내배양시스템을 이용하여 백합의 Fol에 대한 저항성 정도를 효율적으로 검정하는 방법을 확립하고자 하였다. 병원균의 배양조건, 병원균의 식물체 접종 농도, 대상 절편체 종류, 접종 후 적정 발병 기간 등과 같은 조건을 단독, 혹은 조합하여 실험 한 결과 다음의 기내검정조건을 확립하였다. Fol균을 6일 동안 PDA 배지에서 배양한 후 포자 현탁액을 <TEX>$1.0{\times}10^4$</TEX> <TEX>$spores{\cdot}mL^{-1}$</TEX>농도로 조절하여 기내배양 중인 식물체의 잎을 <TEX>$1.5{\times}2.0cm^2$</TEX>의 크기로 절단하여 <TEX>$25^{\circ}C$</TEX>, 암조건에서 22시간 침지시켜 접종하였다. 접종이 끝난 잎절편체는 0.6% 한천배지에 치상하여 온도 <TEX>$25^{\circ}C$</TEX>, 습도 50%, 16시간 광조건(광도 <TEX>$40{\mu}mol{\cdot}m^{-2}{\cdot}s^{-1}$</TEX>)을 유지하면서 병의 발달을 관찰하였다. 발병 정도를 지수화하여 통계처리를 하였다. 기내검정을 통하여 저항성 및 민감성으로 선발한 백합종들을 토양검정법으로 실험한 결과 동일한 저항성 정도를 얻을 수 있었으며, 이는 본 연구에서 확립한 Fol에 대한 구근부패병 기내검정법이 효율적으로 품종 선발에 이용될 수 있음을 보여준다고 하겠다. The soilborne fungus Fusarium oxysporum f. sp. lilii (Fol) is a serious threat to all lily cultivars, especially infecting bulbs and flowers. It has become increasingly important to develop varieties resistant against the bulb rot disease. Genetic diversity of cultivars and reliable screening methods are required for this purpose. Here, an efficient in vitro screening system for evaluating resistance to Fol in 38 in vitro-grown lily plants was investigated. Various factors including culture conditions of Fol, inoculum density, appropriate plant materials, inoculation method and duration, and incubation period of plant materials after inoculation were combined to optimize the screening method. As a result, we suggest optimal conditions for an in vitro screening system for the selection of Fol-resistant lily cultivars as follows. Fol was grown on potato dextrose agar (PDA) medium for 6 days at <TEX>$25^{\circ}C$</TEX> in darkness and used as working inoculation. Spore suspensions were prepared (inoculum density: <TEX>$1.0{\times}10^4$</TEX> <TEX>$spores{\cdot}mL^{-1}$</TEX>), and then leaf segments <TEX>$1.5{\times}2.0cm^2$</TEX> were inoculated by dipping for 22 hours at <TEX>$25^{\circ}C$</TEX> in dark. Later, leaves were cultured on 0.6% agar plates at <TEX>$25^{\circ}C$</TEX> and 50% humidity with a photoperiod of 16 hours light/8 hours dark (fluence rate of <TEX>$40{\mu}mol{\cdot}m^{-2}{\cdot}s^{-1}$</TEX>) to examine the progress of bulb rot. After 7 days, disease levels were classified into indices 1 (no symptom) to 6 (serious bulb rot). Soil inoculation of Fol carried out with resistant or susceptible lily cultivars that had been selected through in vitro screening confirmed the reproducibility of results. Therefore, the in vitro screening method established in this study is efficient and reliable for selection of lily cultivars resistant against bulb rot disease.

Genetic differentiation and gene flow between wild and cultivated Prunus avium: An analysis of molecular genetic evidence at a regional scale

The presence of conspecific wild-type and cultivar populations has been a common landscape feature for centuries. As orchards generally continue to expand towards the natural forest, two important issues are raised: the potential reduction of cultivar genetic diversity compared to wild populations and the extent of gene flow between the two population types. These questions were addressed in a study of Prunus avium in northern Greece using nine simple sequence repeat loci to analyse genetic variation in 93 wild-type individuals and 21 cultivars representing the local cultivated germplasm. Results showed a significant reduction of genetic diversity parameters in the cultivated germplasm compared to natural populations. Bayesian, frequency-based and Markov chain – Monte Carlo analyses have revealed that the wild and cultivar groups are genetically divergent and that realized between-group gene flow is almost completely absent. This result was further verified by a principal component analysis showing a clear separation of the two groups in low multivariate space after a principal coordinate analysis. The significant disjunction in flowering time and a considerable geographic distance between the two groups could primarily account for the absence of substantial gene flow. These findings indicate that local wild cherry can provide a source of genetic variation for future breeding in the genetically restricted cultivar group.

Genetic diversity of storage protein genes in common wheat (Triticum aestivum L.) cultivars from China and its comparison with genetic diversity of cultivars from other countries

Contemporary trends and perspectives of Chinese winter wheat breeding programs were explored using multiple alleles of gliadin (Gli) and glutenin (Glu)-coding loci as genetic markers. To estimate genetic diversity and specific features of Chinese cultivars, the allele frequencies and genetic diversity H in Chinese wheat pool were calculated and compared to those of cultivars from 11 regions of the world. Among all these cultivars the Chinese ones exhibited the highest allelic diversity of the Gli loci while showing relatively low genetic variability for the Glu loci. Most (96%) of the cultivars examined had unique Gli allele compositions, which enabled to differentiate these cultivars with high precision. Cluster analysis of the genetic distances among the wheats from different regions showed that the Chinese cultivars were close to Italian and Russian ones, sharing with them the common Gli alleles. Clustering of modern cultivars and that of cultivars bred 10–15 years ago was essentially the same. All cultivars from all of the countries examined were classified into three groups according to their quality based on their Glu allele compositions. The Chinese cultivars showed a moderate quality score of 7.0, which conforms to the quality evaluation based on SDS sedimentation. This quality proved to be insufficiently high as compared to cultivars from other countries. However, the genetic diversity estimation suggests that Chinese cultivars have a potential for quality improvement.

Assessment of genetic diversity in cultivars and wild accessions of Luohanguo (Siraitia grosvenorii [Swingle] A. M. Lu et Z. Y. Zhang), a species with edible and medicinal sweet fruits endemic to southern China, using RAPD and AFLP markers

Genetic variation of wild populations and cultivars of Luohanguo (Siraitia grosvenorii), a plant species endemic to southern China, was assessed using random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) markers. Based on the results for 130 individuals from seven populations, a high level of genetic diversity of Luohanguo was observed at the species level. The percentage of polymorphic loci (P) was 89.4%, Nei’s gene diversity (He) was 0.239, and Shannon’s information index (Ho) was 0.373 based on the combined AFLP and RAPD data. There was a high degree of genetic differentiation, with 45.1% of the genetic variation attributed to differences between the populations. The genetic diversity of the Luohanguo cultivars is much lower than that of wild populations (P = 41.8%, He = 0.141, Ho = 0.211), and a distinct genetic differentiation is observed between the cultivars and wild accessions. The pool of genetic variation in the wild populations provides an excellent gene resource for Luohanguo breeding.

Assessment of genetic diversity in cultivars of white clover (Trifolium repensL.) detected by SSR polymorphisms

White clover (Trifolium repens L.) is an important temperate pasture legume that plays a key role as a companion to grass species, such as perennial ryegrass (Lolium perenne L.). Due to the outbreeding nature of white clover, cultivars are highly heterogeneous. Genetic diversity was assessed using 16 elite cultivars from Europe, North and South America, Australia, and New Zealand. Fifteen simple sequence repeat markers that detect single, codominant polymorphic genetic loci were selected for the study. The genetic relationships among individuals were compared using phenetic clustering, and those among cultivars were compared using nonmetric multidimensional scaling. Intrapopula tion variability exceeded interpopulation variability, with substantial overlap among populations and weak interpopula tion differentiation. No obvious or significant differentiation was observed on the basis of morphology or geographic origin of the cultivars. The number of parental genotypes used to derive each cultivar was not a major determinant of genome-wide genetic diversity. The outcomes of this assessment of genetic variation in elite white clover germplasm pools have important implications for the feasibility of molecular marker-based cultivar discrimination, and will be used to assist the design of linkage disequilibrium mapping strategies for marker-trait association.

Analysis of cotton genetic diversity by microsatellites and pedigree

The main objective of this study was to verify the association between the coefficient of parentage estimates and multivariate techniques which were used as measures of genetic diversity in cultivars. Thirty cotton cultivars were used for this purpose among which genetic diversity was estimated by means of the parentage coefficient (CP) and also through multivariate techniques employing microsatellite markers (SSR). The correlation between genetic distances obtained by CPs and SSRs for cultivars was positive and significant, with a value of 0.25. The 18 ancestors evaluated in the current study contributed with 69% to the genetic constitution of the 30 cotton cultivars. The evidence that few ancestors actually contribute to the genetic constitution of the cotton cultivars used in Brazil indicates that new alleles should be introduced into the gene pool of these cultivars in order to broaden the genetic base of cotton.

Genealogical analysis of diversity of spring bread wheat cultivars released in Kazakhstan from 1929-2004

The genetic diversity of 116 spring bread wheat cultivars released in Kazakhstan from 1929-2004 was studied by means of a genealogical analysis. The tendency of genetic diversity to change over time was traced by analysing a series of n ´ m matrices, where n is the number of released cultivars and m is the number of landrace ancestors. The pool of landrace ancestors of spring wheat cultivars in 1929-2004 contained a total of 114 landraces and old varieties, including 19 from Kazakhstan and Central Asia and 23 from neighbouring regions of Russia. The original ancestors differ significantly in frequency of presence and hence in their importance in the genepool of spring wheats cultivated in Kazakhstan. Significant differences in the contributions of dominant ancestors to cultivars for various regions have been revealed, showing that those ancestors were specifically adapted to different growing conditions. During the past 75 years, genetic diversity has increased due to the wide use of foreign materials in breeding programmes. A more detailed study has shown that during the period analysed, 15 landraces from Kazakhstan and neighbouring regions of Central Asia and Russia (35% of local germplasm) were lost from the pedigrees. The cluster structure of modern cultivars included in the Kazakhstan Official List (2002) was established. By analysing coefficients of parentage, significant differences in the genetic diversity of cultivars from various growing regions were revealed.

Genetic diversity in cultivars and landraces of Oryza sativa subsp. indica as revealed by AFLP markers.

Genetic diversity among 49 Indian accessions of rice (Oryza sativa subsp. indica), including 29 landraces from Jeypore, 12 modern cultivars, and 8 traditional cultivars from Tamil Nadu, was investigated using AFLP markers. In total, nine primer combinations revealed 664 AFLPs, 408 of which were found to be polymorphic. The percentage of polymorphic AFLPs was approximately the same within the cultivars and landraces. Similar results were obtained when genetic diversity values were estimated using the Shannon-Weiner index of diversity. Genetic diversity was slightly higher in the modern cultivars than in the traditional cultivars from Tamil Nadu. Among the landraces from Jeypore, the lowland landraces showed the highest diversity. The present study showed that the process of breeding modern cultivars did not appear to cause significant genetic erosion in rice. Cluster analysis and the first component of principle component analysis (PCA) both showed a clear demarcation between the cultivars and landraces as separate groups, although the genetic distance between them was narrow. The modern cultivars were positioned between the landraces from Jeypore and the traditional cultivars from Tamil Nadu. The second component of PCA further separated medium and upland landraces from lowland landraces, with the lowland landraces found closest to the traditional and modern cultivars.

Assessing genetic diversity in the cassava (Manihot esculenta Crantz) germplasm collection in Brazil using PCR-based markers

Knowledge of the origin, organization and nature of the cassava (Manihot esculenta Crantz) germplasm collection in Brazil is incomplete due to lack of critical information on several aspects of the collection. This study verifies the utility of SSR-primed PCR markers for germplasm assessment and then utilizes these markers as well as RAPD's to characterize the Brazilian collection. We specifically address the following questions: 1)what is the relationship of morphologically closely related species to cultivated cassava? 2) What is the genetic diversity of cultivars within and between different habitats in Brazil? 3) Do agronomic traits and molecular markers reveal the same relationship among cassava accessions? 4) How complete is the Brazilian cassava collection and how well is it represented in the Word Core Collection of cassava, maintained by CIAT? Results of the interspecific studies of cassava and its wild relatives confirms the close relationship of cassava, Manihot esculenta ssp. esculenta to Manihot esculenta ssp. flabellifolia as well identifying several other closely related wild species. Next, PCR-based markers indicate a strong grouping of varieties related to the region of cultivation in Brazil. Moreover, important regions such as Cerrados and Amazon are relatively poorly represented in germplasm collections. Interestingly, the relationships of accessions based on agronomic traits are not fully congruent with relationships revealed with RAPD markers. Finally, the genetic diversity of the Brazilian cassava collection is not fully represented in the Core of the Word Core Collection of CIAT.