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      Genotype × Environment Studies on Resistance to Late Leaf Spot and Rust in Genomic Selection Training Population of Peanut ( Arachis hypogaea L.)

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          Abstract

          Foliar fungal diseases especially late leaf spot (LLS) and rust are the important production constraints across the peanut growing regions of the world. A set of 340 diverse peanut genotypes that includes accessions from gene bank of International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), elite breeding lines from the breeding program, and popular cultivars were screened for LLS and rust resistance and yield traits across three locations in India under natural and artificial disease epiphytotic conditions. The study revealed significant variation among the genotypes for LLS and rust resistance at different environments. Combined analysis of variance revealed significant environment (E) and genotype × environment (G×E) interactions for both the diseases indicating differential response of genotypes in different environments. The present study reported 31 genotypes as resistant to LLS and 66 to rust across the locations at 90 DAS with maturity duration 103 to 128 days. Twenty-eight genotypes showed resistance to both the diseases across the locations, of which 19 derived from A. cardenasii, five from A. hypogaea, and four from A. villosa. Site regression and Genotype by Genotype x Environment (GGE) biplot analysis identified eight genotypes as stable for LLS, 24 for rust and 14 for pod yield under disease pressure across the environments. Best performing environment specific genotypes were also identified. Nine genotypes resistant to LLS and rust showed 77% to 120% increase in pod yield over control under disease pressure with acceptable pod and kernel features that can be used as potential parents in LLS and rust resistance breeding. Pod yield increase as a consequence of resistance offered to foliar fungal diseases suggests the possibility of considering ‘foliar fungal disease resistance’ as a must-have trait in all the peanut cultivars that will be released for cultivation in rainfed ecologies in Asia and Africa. The phenotypic data of the present study will be used for designing genomic selection prediction models in peanut.

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          Cultivar Evaluation and Mega-Environment Investigation Based on the GGE Biplot

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            A QTL study on late leaf spot and rust revealed one major QTL for molecular breeding for rust resistance in groundnut (Arachis hypogaea L.)

            Late leaf spot (LLS) and rust are two major foliar diseases of groundnut (Arachis hypogaea L.) that often occur together leading to 50–70% yield loss in the crop. A total of 268 recombinant inbred lines of a mapping population TAG 24 × GPBD 4 segregating for LLS and rust were used to undertake quantitative trait locus (QTL) analysis. Phenotyping of the population was carried out under artificial disease epiphytotics. Positive correlations between different stages, high to very high heritability and independent nature of inheritance between both the diseases were observed. Parental genotypes were screened with 1,089 simple sequence repeat (SSR) markers, of which 67 (6.15%) were found polymorphic. Segregation data obtained for these markers facilitated development of partial linkage map (14 linkage groups) with 56 SSR loci. Composite interval mapping (CIM) undertaken on genotyping and phenotyping data yielded 11 QTLs for LLS (explaining 1.70–6.50% phenotypic variation) in three environments and 12 QTLs for rust (explaining 1.70–55.20% phenotypic variation). Interestingly a major QTL associated with rust (QTLrust01), contributing 6.90–55.20% variation, was identified by both CIM and single marker analysis (SMA). A candidate SSR marker (IPAHM 103) linked with this QTL was validated using a wide range of resistant/susceptible breeding lines as well as progeny lines of another mapping population (TG 26 × GPBD 4). Therefore, this marker should be useful for introgressing the major QTL for rust in desired lines/varieties of groundnut through marker-assisted backcrossing. Electronic supplementary material The online version of this article (doi:10.1007/s00122-010-1366-x) contains supplementary material, which is available to authorized users.
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              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. Electronic supplementary material The online version of this article (doi:10.1007/s11032-011-9661-z) contains supplementary material, which is available to authorized users.
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                Author and article information

                Contributors
                Journal
                Front Plant Sci
                Front Plant Sci
                Front. Plant Sci.
                Frontiers in Plant Science
                Frontiers Media S.A.
                1664-462X
                04 December 2019
                2019
                : 10
                : 1338
                Affiliations
                [1] 1Crop Improvement- Asia Program, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) , Hyderabad, India
                [2] 2Department of Plant Breeding and Genetics, Jawaharlal Nehru Krishi Vishwa Vidyalaya (JNKVV) , Jabalpur, India
                [3] 3Oilseeds Research Station, Mahatma Phule Krishi Vidyapeeth (MPKV) , Jalgaon, India
                [4] 4Coconut Research Station, Tamil Nadu Agricultural University (TNAU) , Coimbatore, India
                [5] 5Department of Biotechnology, University of Agricultural Sciences , Dharwad, India
                Author notes

                Edited by: Jose C. Jimenez-Lopez, Consejo Superior de Investigaciones Científicas (CSIC) Granada, Spain

                Reviewed by: Suvendu Mondal, Bhabha Atomic Research Centre (BARC), India; Pei Xu, China Jiliang University, China; Muthukrishnan Sathiyabama, Bharathidasan University, India

                *Correspondence: Janila Pasupuleti, p.janila@ 123456cgiar.org

                This article was submitted to Plant Breeding, a section of the journal Frontiers in Plant Science

                Article
                10.3389/fpls.2019.01338
                6904303
                31867023
                59525ee3-b6e8-4dfd-b969-1d3d9cb1e2a8
                Copyright © 2019 Chaudhari, Khare, Patil, Sundravadana, Variath, Sudini, Manohar, Bhat and Pasupuleti

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 15 May 2019
                : 25 September 2019
                Page count
                Figures: 5, Tables: 3, Equations: 1, References: 49, Pages: 14, Words: 8996
                Categories
                Plant Science
                Original Research

                Plant science & Botany
                g x e,gge,genomic selection,peanut,training population
                Plant science & Botany
                g x e, gge, genomic selection, peanut, training population

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