Genetic diversity of peanut (Arachis hypogaea L.) and its wild relatives based on the analysis of hypervariable regions of the genome

BACKGROUND: The genus Arachis is native to a region that includes Central Brazil and neighboring countries. Little is known about the genetic variability of the Brazilian cultivated peanut (Arachis hypogaea, genome AABB) germplasm collection at the DNA level. The understanding of the genetic diversity of cultivated and wild species of peanut (Arachis spp.) is essential to develop strategies of collection, conservation and use of the germplasm in variety development. The identity of the ancestor progenitor species of cultivated peanut has also been of great interest. Several species have been suggested as putative AA and BB genome donors to allotetraploid A. hypogaea. Microsatellite or SSR (Simple Sequence Repeat) markers are co-dominant, multiallelic, and highly polymorphic genetic markers, appropriate for genetic diversity studies. Microsatellite markers may also, to some extent, support phylogenetic inferences. Here we report the use of a set of microsatellite markers, including newly developed ones, for phylogenetic inferences and the analysis of genetic variation of accessions of A. hypogea and its wild relatives. RESULTS: A total of 67 new microsatellite markers (mainly TTG motif) were developed for Arachis. Only three of these markers, however, were polymorphic in cultivated peanut. These three new markers plus five other markers characterized previously were evaluated for number of alleles per locus and gene diversity using 60 accessions of A. hypogaea. Genetic relationships among these 60 accessions and a sample of 36 wild accessions representative of section Arachis were estimated using allelic variation observed in a selected set of 12 SSR markers. Results showed that the Brazilian peanut germplasm collection has considerable levels of genetic diversity detected by SSR markers. Similarity groups for A. hypogaea accessions were established, which is a useful criteria for selecting parental plants for crop improvement. Microsatellite marker transferability was up to 76% for species of the section Arachis, but only 45% for species from the other eight Arachis sections tested. A new marker (Ah-041) presented a 100% transferability and could be used to classify the peanut accessions in AA and non-AA genome carriers. CONCLUSION: The level of polymorphism observed among accessions of A. hypogaea analyzed with newly developed microsatellite markers was low, corroborating the accumulated data which show that cultivated peanut presents a relatively reduced variation at the DNA level. A selected panel of SSR markers allowed the classification of A. hypogaea accessions into two major groups. The identification of similarity groups will be useful for the selection of parental plants to be used in breeding programs. Marker transferability is relatively high between accessions of section Arachis. The possibility of using microsatellite markers developed for one species in genetic evaluation of other species greatly reduces the cost of the analysis, since the development of microsatellite markers is still expensive and time consuming. The SSR markers developed in this study could be very useful for genetic analysis of wild species of Arachis, including comparative genome mapping, population genetic structure and phylogenetic inferences among species

Diversity Analysis of Elite Maize Inbred Lines Adapted to West and Central Africa Using SSR Markers

Seventeen elite maize inbred lines of West and Central Africa adaptation with tropical and temperate x tropical origin were investigated for diversity at 18 SSR loci in non-coding regions of the maize genome, alongside two temperate inbred lines (B73 and Mo17), perennial teosinte (Zea diploperennis) and gamagrass (Tripsacum dactyloides). A total of 174 alleles were detected with a range of 5 to 15 alleles per maker and an average of 9.7 alleles per locus. Polymorphic information content (PIC) ranged from 0.29 in umc1226 to 0.92 in bnlg2122 with an average of 0.75. Relationships between heterotic groups and groups based on SSR data were quite varied for the lines studied. Primarily, the SSR markers grouped the lines on the basis of their origin, with three instances of a pair of heterotic lines clustering together; one pair of temperate origin and the other two tropical vs temperate x tropical. Four inbred lines (CMR 19, CMR 20, CMR 21, and CMR 26), belonging to three heterotic groups were, however, differentiated by SSR data. The markers showed potential for use in managing inbred lines germplasm adapted to West and Central Africa, particularly for classifying inbred lines for which records of ancestry are not readily available and for exploiting the heterosis known for tropical vs. temperate x tropical crosses

Molecular Diversity, Structure and Domestication of Grasses

Over the last 10,000 years, crop domestication has been the single most important human cultural development. Grasses are prominent among these crops, and provide the vast majority of the world\u27s food. Similar traits have been selected during the domestication and breeding of these critically important grasses, and since they share a similar complement of genes, the same set of genes may have been selected. Even though the process of domestication occurred over the same 5000 to 10,000 year period, the domesticated grasses have major differences in genome structure, diversity, and life history. Molecular investigations of grass domestication have succeeded in identifying progenitor species and are beginning to catalog genetic resources. Additionally, research is now elucidating some of the basic processes by which crops have evolved over the last few millennia. In this review, we discuss our present knowledge of molecular diversity among the grass crops and relate that diversity to the genes involved in domestication and to yield gains. Understanding the connection between diversity and genome structure will be critical to future crop breeding

Sorghum and Pearl Millet Genetic Resources Utilization

Sorghum and pearl millet are unique in size and diversity. The largest collections contain 40,570 (U.S. sorghum collection) and21,191 (ICR1SATpearl millet collection) accessions. Less than three percent of these accessions have been used in crop improvement. Curation— or acquisition, maintenance, characterization, and utilization—plays a role in exploitation o f the genetic variation within these collections. Cultivation of sorghum andpearl millet is increasing the use of marginal agricultural land. Future utilization will depend on increased research on abiotic and biotic stress tolerance. To facilitate exploitation o f this vast germplasm, traditional and biotechnical methods must be combined to provide better understanding of the genetic variation available, which then can be used in crop enhancement. This can only be accomplished through sharing of ideas, particularly through creation of an arena where information is globally accessible

Molecular tools in plant genetic resources conservation: A guide to the technologies

In October 1995, IPGRI organized a small workshop on the use of molecular techniques in the conservation of plant genetic resources. One area of discussion was the considerable range of different molecular techniques available and the ways in which they could best be used. Deciding on which technique would be most appropriate for particular investigations is not always straightforward and depends on a range of a different factors including the nature of the problem, the biology of the species and the resources available. A number of the experts who participated in the meeting collaborated with IPGRI staff to prepare this publication, which attempts to provide a brief overview of currently available techniques and to outline some of their strengths and limitations. It also provides a framework to assist users in identifying what technique(s) might be most appropriate for their own needs. It is not intended as a laboratory manual of the techniques or as a substitute for the many excellent discussions of the strengths and weaknesses of individual methods that can be found in the literature. Rather, it is a broad survey of the main features of the different techniques and of the factors that conservation workers should bear in mind when initiating a molecular genetic based investigation

Meta-analysis identifies pleiotropic loci controlling phenotypic trade-offs in sorghum

Community association populations are composed of phenotypically and genetically diverse accessions. Once these populations are genotyped, the resulting marker data can be reused by different groups investigating the genetic basis of different traits. Because the same genotypes are observed and scored for a wide range of traits in different environments, these populations represent a unique resource to investigate pleiotropy. Here, we assembled a set of 234 separate trait datasets for the Sorghum Association Panel, a group of 406 sorghum genotypes widely employed by the sorghum genetics community. Comparison of genome-wide association studies (GWAS) conducted with two independently generated marker sets for this population demonstrate that existing genetic marker sets do not saturate the genome and likely capture only 35–43% of potentially detectable loci controlling variation for traits scored in this population. While limited evidence for pleiotropy was apparent in cross-GWAS comparisons, a multivariate adaptive shrinkage approach recovered both known pleiotropic effects of existing loci and new pleiotropic effects, particularly significant impacts of known dwarfing genes on root architecture. In addition, we identified new loci with pleiotropic effects consistent with known trade-offs in sorghum development. These results demonstrate the potential for mining existing trait datasets from widely used community association populations to enable new discoveries from existing trait datasets as new, denser genetic marker datasets are generated for existing community association populations

Genome-Wide Association Study of Grain Polyphenol Concentrations in Global Sorghum [Sorghum bicolor (L.) Moench] Germplasm

Identifying natural variation of health-promoting compounds in staple crops and characterizing its genetic basis can help improve human nutrition through crop biofortification. Some varieties of sorghum, a staple cereal crop grown worldwide, have high concentrations of proanthocyanidins and 3-deoxyanthocyanidins, polyphenols with antioxidant and anti-inflammatory properties. We quantified total phenols, proanthocyanidins, and 3-deoxyanthocyanidins in a global sorghum diversity panel (n = 381) using near-infrared spectroscopy (NIRS), and characterized the patterns of variation with respect to geographic origin and botanical race. A genome-wide association study (GWAS) with 404,628 SNP markers identified novel quantitative trait loci for sorghum polyphenols, some of which colocalized with homologues of flavonoid pathway genes from other plants, including an orthologue of maize (Zea mays) Pr1 and a homologue of Arabidopsis (Arabidopsis thaliana) TT16. This survey of grain polyphenol variation in sorghum germplasm and catalog of flavonoid pathway loci may be useful to guide future enhancement of cereal polyphenols

Microsatellite identification and characterization in peanut (A. hypogaea L.)

A major constraint to the application of biotechnology to the improvement of the allotetraploid peanut, or groundnut (Arachis hypogaea L.), has been the paucity of polymorphism among germplasm lines using biochemical (seed proteins, isozymes) and DNA markers (RFLPs and RAPDs). Six sequence-tagged microsatellite (STMS) markers were previously available that revealed polymorphism in cultivated peanut. Here, we identify and characterize 110 STMS markers that reveal genetic variation in a diverse array of 24 peanut landraces. The simple-sequence repeats (SSRs) were identified with a probe of two 27,648-clone genomic libraries: one constructed using PstI and the other using Sau3AI/BamHI. The most frequent, repeat motifs identified were ATT and GA, which represented 29% and 28%, respectively, of all SSRs identified. These were followed by AT, CTT, and GT. Of the amplifiable primers, 81% of ATT and 70.8% of GA repeats were polymorphic in the cultivated peanut test array. The repeat motif AT showed the maximum number of alleles per locus (5.7). Motifs ATT, GT, and GA had a mean number of alleles per locus of 4.8, 3.8, and 3.6, respectively. The high mean number of alleles per polymorphic locus, combined with their relative frequency in the genome and amenability to probing, make ATT and GA the most useful and appropriate motifs to target to generate further SSR markers for peanut

The complete nucleotide sequence and genome organization of the M RNA segment of peanut bud necrosis tospovirus and comparison with other tospoviruses

The M RNA of peanut bud necrosis tospovirus is 4801 nucleotides in length. It comprised 2 ORFs in an ambisense organization and terminal inverted repeats. The 3 prime large ORF (3363 nucleotides in the virus-complementary strand) encoded a protein with a predicted size of 127.2 kDa which was identified as the glycoprotein precursor (GP) of the G1 and G2 glycoproteins. A comparison of the deduced amino acid sequence of GP revealed 37% identity and 58-59% similarity with that of tomato spotted wilt tospovirus (TSWV,serogroup I) and impatiens necrotic spot tospovirus (INSV, serogroup III) and 21-23% identity and 44-47% similarity with members of the genus Bunyavirus. The 5 prime small ORF (924 nucleotides in the virus-sense strand) encoded a 34.2 kDa protein which was identified as the non-structural (NSm) protein based on 41-43% identity and 60-63% similarity with TSWV and INSV. Defective RNA molecules derived from the genomic M RNA were detected during continuous passage of the virus by sap inoculations