Construction of a genetic linkage map and QTL analysis for late leaf spot and rust in groundnut (Arachis hypogaea L.)

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Genetic enhancement of resistance to foliar diseases - strategies and prospects

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Marker-assisted introgression of a QTL region to improve rust resistance in three elite and popular varieties of peanut (Arachis hypogaea L.)

Leaf rust, caused by Puccinia arachidis Speg, is one of the major devastating diseases in peanut (Arachis hypogaea L.). One QTL region on linkage group AhXV explaining upto 82.62 % phenotypic variation for rust resistance was validated and introgressed from cultivar ‘GPBD 4’ into three rust susceptible varieties (‘ICGV 91114’, ‘JL 24’ and ‘TAG 24’) through marker-assisted backcrossing (MABC). The MABC approach employed a total of four markers including one dominant (IPAHM103) and three co-dominant (GM2079, GM1536, GM2301) markers present in the QTL region. After 2–3 backcrosses and selfing, 200 introgression lines (ILs) were developed from all the three crosses. Field evaluation identified 81 ILs with improved rust resistance. Those ILs had significantly increased pod yields (56–96 %) in infested environments compared to the susceptible parents. Screening of selected 43 promising ILs with 13 markers present on linkage group AhXV showed introgression of the target QTL region from the resistant parent in 11 ILs. Multi-location field evaluation of these ILs should lead to the release of improved varieties. The linked markers may be used in improving rust resistance in peanut breeding programmes

Identification of quantitative trait loci for protein content, oil content and oil quality for groundnut (Arachis hypogaea L.)

Very few efforts have been made to improve the nutritional quality of groundnut, as biochemical estimation of quality traits is laborious and uneconomic; hence, it is difficult to improve them through traditional breeding alone. Identification of molecular markers for quality traits will have a great impact in molecular breeding. An attempt was made to identify microsatellite or simple sequence repeat (SSR) markers for important nutritional traits (protein content, oil content and oil quality in terms of oleic acid, linoleic acid and oleic/linoleic acid ratio) in a mapping population consisting of 146 recombinant inbreed lines (RILs) of a cross TG26 × GPBD4. Phenotyping data analysis for quality traits showed significant variation in the population and environment, genotype × environment interaction and high heritability was observed for all the traits. Negative correlation between protein content and oil content, oleic acid and linoleic acid indicated their antagonistic nature. After screening >1000 SSR markers, a partial genetic linkage map comprising of 45 SSR loci on 8 linkage groups with an average inter-marker distance of 14.62 cM was developed. QTL analysis based on single marker analysis (SMA) and composite interval mapping identified some candidate SSR markers associated with major QTLs as well as several minor QTLs for the nutritional traits. Validation of these major QTLs using a wider genetic background may provide the markers for molecular breeding for improving groundnut for nutritional traits

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Not AvailableFinger millet is an excellent source of mineral elements specifically calcium and iron. The iron content in the ruling variety, GPU-28 is 5.47 mg/100g. Identification of germplasm lines superior to GPU-28 would help in identifying nutritionally superior genotypes and also to serve as genetic resource for recombination breeding. For such screening, use of appropriate procedure and bench mark values are highly useful. Hence, the present study was conducted to confirm the estimation procedure and to arrive at bench mark values for grain iron content in popular varieties. The elemental analysis was carried out in two laboratories. The results of the study indicated a positive correlation between the two laboratories for iron content and confirmed the appropriateness of procedure used for digestion and AAS estimation. Among the varieties, the iron content was significantly superior in GPU-67 (6.52 mg/100g) compared to the GPU-28 and hence, this variety and grain iron content can be considered as a variety with bench mark value for screening large number of germplasm lines.Not Availabl

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Characterization of AhMITE1 transposition and its association with the mutational and evolutionary origin of botanical types in peanut (Arachis spp.)

AhMITE1 is an active miniature inverted repeat transposable element (MITE) in peanut (Arachis hypogaea L). Its transpositional activity from a particular (FST1-linked) site within the peanut genome was checked using AhMITE1-specifc PCR, which used a forward primer annealing to the 5′-flanking sequence and a reverse primer binding to AhMITE1. It was found that transposition activation was induced by stresses such as ethyl methane sulfonate (EMS), gamma irradiation, environmental conditions, and tissue culture. Excision and insertion of AhMITE1 at this particular site among the mutants led to gross morphological changes resembling alternate subspecies or botanical types. Analysis of South American landraces revealed the presence of AhMITE1 at the site among most of the spp. fastigiata types, whereas the element was predominantly missing from spp. hypogaea types, indicating its strong association. Four accessions of the primitive allotetraploid, A. monticola were devoid of AhMITE1 at the site, indicating only recent activation of the element, possibly because of the “genomic shock” resulting from hybridization followed by allopolyploidization

Sequencing analysis of genetic loci for resistance for late leaf spot and rust in peanut (Arachis hypogaea L.)

The aim of this study was to identify candidate resistance genes for late leaf spot (LLS) and rust diseases in peanut (Arachis hypogaea L.). We used a double-digest restriction-site associated DNA sequencing (ddRAD-Seq) technique based on next-generation sequencing (NGS) for genotyping analysis across the recombinant inbred lines (RILs) derived from a cross between a susceptible line, TAG 24, and a resistant line, GPBD 4. A total of 171 SNPs from the ddRAD-Seq together with 282 markers published in the previous studies were mapped on a genetic map covering 1510.1 cM. Subsequent quantitative trait locus (QTL) analysis revealed major genetic loci for LLS and rust resistance on chromosomes A02 and A03, respectively. Heterogeneous inbred family-derived near isogenic lines and the pedigree of the resistant gene donor, A. cardenasii Krapov. & W.C. Greg., including the resistant derivatives of ICGV 86855 and VG 9514 as well as GPBD 4, were employed for whole-genome resequencing analysis. The results indicated the QTL candidates for LLS and rust resistance were located in 1.4- and 2.7-Mb genome regions on A02 and A03, respectively. In these regions, four and six resistance-related genes with deleterious mutations were selected as candidates for LLS and rust resistance, respectively. These delimited genomic regions may be beneficial in breeding programs aimed at improving disease resistance and enhancing peanut productivity

Quantitative trait locus analysis and construction of consensus genetic map for foliar disease resistance based on two recombinant inbred line populations in cultivated groundnut (Arachis hypogaea L.)

Late leaf spot (LLS) and rust have the greatest impact on yield losses worldwide in groundnut (Arachis hypogaea L.). With the objective of identifying tightly linked markers to these diseases, a total of 3,097 simple sequence repeats (SSRs) were screened on the parents of two recombinant inbred line (RIL) populations, namely TAG 24 × GPBD 4 (RIL-4) and TG 26 × GPBD 4 (RIL-5), and segregation data were obtained for 209 marker loci for each of the mapping populations. Linkage map analysis of the 209 loci resulted in the mapping of 188 and 181 loci in RIL-4 and RIL-5 respectively. Using 143 markers common to the two maps, a consensus map with 225 SSR loci and total map distance of 1,152.9 cM was developed. Comprehensive quantitative trait locus (QTL) analysis detected a total of 28 QTL for LLS and 15 QTL for rust. A major QTL for LLS, namely QTLLLS01 (GM1573/GM1009-pPGPseq8D09), with 10.27–62.34% phenotypic variance explained (PVE) was detected in all the six environments in the RIL-4 population. In the case of rust resistance, in addition to marker IPAHM103 identified earlier, four new markers (GM2009, GM1536, GM2301 and GM2079) showed significant association with the major QTL (82.96% PVE). Localization of 42 QTL for LLS and rust on the consensus map identified two candidate genomic regions conferring resistance to LLS and rust. One region present on linkage group AhXV contained three QTL each for LLS (up to 67.98% PVE) and rust (up to 82.96% PVE). The second candidate genomic region contained the major QTL with up to 62.34% PVE for LLS. Molecular markers associated with the major QTL for resistance to LLS and rust can be deployed in molecular breeding for developing groundnut varieties with enhanced resistance to foliar diseases