SSR-based genetic linkage map for cultivated groundnut (Arachis hypogaea L.) for QTL analysis and comparative mapping

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The first SSR-based genetic linkage map for cultivated groundnut (Arachis hypogaea L.)

Molecular markers and genetic linkage maps are pre-requisites for molecular breeding in any crop species. In case of peanut or groundnut (Arachis hypogaea L.), an amphidiploid (4X) species, not a single genetic map is, however, available based on a mapping population derived from cultivated genotypes. In order to develop a genetic linkage map for tetraploid cultivated groundnut, a total of 1,145 microsatellite or simple sequence repeat (SSR) markers available in public domain as well as unpublished markers from several sources were screened on two genotypes, TAG 24 and ICGV 86031 that are parents of a recombinant inbred line mapping population. As a result, 144 (12.6%) polymorphic markers were identified and these amplified a total of 150 loci. A total of 135 SSR loci could be mapped into 22 linkage groups (LGs). While six LGs had only two SSR loci, the other LGs contained 3 (LG_AhXV) to 15 (LG_AhVIII) loci. As the mapping population used for developing the genetic map segregates for drought tolerance traits, phenotyping data obtained for transpiration, transpiration efficiency, specific leaf area and SPAD chlorophyll meter reading (SCMR) for 2 years were analyzed together with genotyping data. Although, 2–5 QTLs for each trait mentioned above were identified, the phenotypic variation explained by these QTLs was in the range of 3.5–14.1%. In addition, alignment of two linkage groups (LGs) (LG_AhIII and LG_AhVI) of the developed genetic map was shown with available genetic maps of AA diploid genome of groundnut and Lotus and Medicago. The present study reports the construction of the first genetic map for cultivated groundnut and demonstrates its utility for molecular mapping of QTLs controlling drought tolerance related traits as well as establishing relationships with diploid AA genome of groundnut and model legume genome species. Therefore, the map should be useful for the community for a variety of applications

High-density genetic map using whole-genome resequencing for fine mapping and candidate gene discovery for disease resistance in peanut

Whole‐genome resequencing (WGRS) of mapping populations has facilitated development of high‐density genetic maps essential for fine mapping and candidate gene discovery for traits of interest in crop species. Leaf spots, including early leaf spot (ELS) and late leaf spot (LLS), and Tomato spotted wilt virus (TSWV) are devastating diseases in peanut causing significant yield loss. We generated WGRS data on a recombinant inbred line population, developed a SNP‐based high‐density genetic map, and conducted fine mapping, candidate gene discovery and marker validation for ELS, LLS and TSWV. The first sequence‐based high‐density map was constructed with 8869 SNPs assigned to 20 linkage groups, representing 20 chromosomes, for the ‘T’ population (Tifrunner × GT‐C20) with a map length of 3120 cM and an average distance of 1.45 cM. The quantitative trait locus (QTL) analysis using high‐density genetic map and multiple season phenotyping data identified 35 main‐effect QTLs with phenotypic variation explained (PVE) from 6.32% to 47.63%. Among major‐effect QTLs mapped, there were two QTLs for ELS on B05 with 47.42% PVE and B03 with 47.38% PVE, two QTLs for LLS on A05 with 47.63% and B03 with 34.03% PVE and one QTL for TSWV on B09 with 40.71% PVE. The epistasis and environment interaction analyses identified significant environmental effects on these traits. The identified QTL regions had disease resistance genes including R‐genes and transcription factors. KASP markers were developed for major QTLs and validated in the population and are ready for further deployment in genomics‐assisted breeding in peanut

The coat protein of arabis mosaic virus and it's expression in plants, insect cells and bacteria

SIGLEAvailable from British Library Document Supply Centre- DSC:D170975 / BLDSC - British Library Document Supply CentreGBUnited Kingdo

The coat protein of arabis mosaic virus and it's expression in plants, insect cells and bacteria

SIGLEAvailable from British Library Document Supply Centre- DSC:D170975 / BLDSC - British Library Document Supply CentreGBUnited Kingdo

Identification of candidate genome regions controlling disease resistance in Arachis

Background Worldwide, diseases are important reducers of peanut (Arachis hypogaea) yield. Sources of resistance against many diseases are available in cultivated peanut genotypes, although often not in farmer preferred varieties. Wild species generally harbor greater levels of resistance and even apparent immunity, although the linkage of agronomically un-adapted wild alleles with wild disease resistance genes is inevitable. Marker-assisted selection has the potential to facilitate the combination of both cultivated and wild resistance loci with agronomically adapted alleles. However, in peanut there is an almost complete lack of knowledge of the regions of the Arachis genome that control disease resistance. Results In this work we identified candidate genome regions that control disease resistance. For this we placed candidate disease resistance genes and QTLs against late leaf spot disease on the genetic map of the A-genome of Arachis, which is based on microsatellite markers and legume anchor markers. These marker types are transferable within the genus Arachis and to other legumes respectively, enabling this map to be aligned to other Arachis maps and to maps of other legume crops including those with sequenced genomes. In total, 34 sequence-confirmed candidate disease resistance genes and five QTLs were mapped. Conclusion Candidate genes and QTLs were distributed on all linkage groups except for the smallest, but the distribution was not even. Groupings of candidate genes and QTLs for late leaf spot resistance were apparent on the upper region of linkage group 4 and the lower region of linkage group 2, indicating that these regions are likely to control disease resistance

QTLs from genome to field using markers and genetic maps for peanut improvement : W217

Peanut (Arachis hypogaea) is widely grown in the semi-arid tropics regions of Asia, Africa and Latin America where several stress factors together adversely affect productivity. Collaborative efforts led development of large scale genomic resources setting platform for genomics-assisted breeding (GAB). GAB promises to foster genetic enhancement leading to increased productivity, drought tolerance, disease resistance and improved oil quality in groundnut which are otherwise difficult through conventional breeding alone. In this context, after screening a total of 4,245 SSR markers on parental genotypes of five mapping populations, individual genetic maps with 83-191 marker loci were constructed. Using marker segregation data from 11 populations, a reference consensus genetic map was developed with 897 marker loci which was then further enriched upto 3,693 marker loci by adding mapping information from five new genetic maps. Detailed QTL analyses provided 153 QTLs for drought tolerance related traits, 43 QTLs for foliar diseases (late leaf spot and leaf rust) and 49 QTLs for oil quality. A major QTL contributing upto 82.96% phenotypic variation for rust resistance has been introgressed into three elite peanut varieties namely ICGV 91114, JL 24 and TAG 24 using marker-assisted backcrossing. Disease screening of 200 introgression lines in advanced generation (117 BC2F5 and 83 BC3F5) have recorded a rust score of 2 (scale 1 to 9). The promising lines with desirable yield and higher resistance to leaf rust could be released an improved varieties. Integration of such genomics approaches in breeding programme will enhance crop productivity of groundnut

Development and evaluation of a high density genotyping ‘Axiom_Arachis’ array with 58 K SNPs for accelerating genetics and breeding in groundnut

Single nucleotide polymorphisms (SNPs) are the most abundant DNA sequence variation in the genomes which can be used to associate genotypic variation to the phenotype. Therefore, availability of a high-density SNP array with uniform genome coverage can advance genetic studies and breeding applications. Here we report the development of a high-density SNP array ‘Axiom_Arachis’ with 58 K SNPs and its utility in groundnut genetic diversity study. In this context, from a total of 163,782 SNPs derived from DNA resequencing and RNA-sequencing of 41 groundnut accessions and wild diploid ancestors, a total of 58,233 unique and informative SNPs were selected for developing the array. In addition to cultivated groundnuts (Arachis hypogaea), fair representation was kept for other diploids (A. duranensis, A. stenosperma, A. cardenasii, A. magna and A. batizocoi). Genotyping of the groundnut ‘Reference Set’ containing 300 genotypes identified 44,424 polymorphic SNPs and genetic diversity analysis provided in-depth insights into the genetic architecture of this material. The availability of the high-density SNP array ‘Axiom_Arachis’ with 58 K SNPs will accelerate the process of high resolution trait genetics and molecular breeding in cultivated groundnut

Marker-Assisted Selection for Biotic Stress Resistance in Peanut

Marker-assisted selection (MAS) in peanut has lagged behind other major crops. This is due in good part to the genetic bottleneck that occurred at tetraploidization, resulting in a limited amount of molecular variability detectable among accessions of the cultivated species. However, marker maps have been developed from wild species, and, to an increasing extent, the cultivated species using new marker types. It is expected that, with the increase in number of simple sequence repeat (SSR) markers and development of single nucleotide polymorphism (SNP)-based markers, there will be greater use of MAS in both interspecific and cultivated accession crosses. MAS has already proven itself to be useful in developing cultivars possessing resistance to the root-knot nematode, and is being used for selection for resistance to late leaf spot and rust, as well as for the high-oleic-acid trait

Molecular Markers, Genetic Maps and QTLs for Molecular Breeding in Peanut

Peanut or groundnut (Arachis hypogaea L.), with current annual production of 38.0 million tons from an area of 24.0 m ha (http://faostat.fao.org), is the fourth-largest oilseed crop in the world and is mostly grown in semiarid regions with relatively low inputs of chemical fertilizers. The crop is cultivated in more than 100 countries of Asia, Africa and the Americas with the largest (more than two-third) contributions coming from China and India. Peanut plays important roles in food and nutritional security along with improving the livelihood of resource-poor farmers. Peanut seeds contain edible oil (40-60%), protein (20-40%), carbohydrate (10-20%) and several nutritional components such as vitamin E, niacin, calcium, phosphorus, magnesium, zinc, iron, ribofl avin, thiamine and potassium. Several uses of peanut make it an excellent cash crop for domestic as well as international trade. The major share goes towards extraction of vegetable oil for use in cooking apart from its use in the confectionary industry and fodder, a major source for protein feed for animals