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Bomma N, Shruthi HB, Soregaon CD, Gaddameedi A, Suma K, Pranati J, Chandappa LH, Patil DK, Kumar N, Sandeep S, Vemula A, Gangashetty PI. Multi-environment testing for G×E interactions and identification of high-yielding, stable, medium-duration pigeonpea genotypes employing AMMI, GGE biplot, and YREM analyses. FRONTIERS IN PLANT SCIENCE 2024; 15:1396826. [PMID: 39100084 PMCID: PMC11295248 DOI: 10.3389/fpls.2024.1396826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 06/05/2024] [Indexed: 08/06/2024]
Abstract
Pigeonpea [Cajanus cajan (L.) Millspaugh] is a widely grown pulse with high seed protein content that contributes to food and nutritional security in the Indian subcontinent. The majority of pigeonpea varieties cultivated in India are of medium duration (<180 days to maturity), which makes it essential for breeders to focus on the development of stable high-yielding varieties. The diverse agroecological regime in the Indian subcontinent necessitates an efficient multi-environment study by taking into consideration genotype (G) × environment (E) interaction (GEI) that has a significant impact on traits like grain yield (GY) in developing high-yielding and widely adaptable varieties. In the present study, 37 pigeonpea genotypes were evaluated during the 2021 rainy season at ARS Badnapur, ARS Tandur, BAU Ranchi, GKVK Bengaluru, and ICRISAT Patancheru. The GEI was significant on the grain yield (p < 0.01), and hence, genotype + genotype × environment (GGE) and additive main effects and multiplicative interaction (AMMI) biplots along with AMMI stability value (ASV) and yield relative to environmental maximum (YREM) statistics were used to identify stable high-yielding genotypes. The interaction principal component analysis 1 and 2 (IPC1 and IPC2) explained 40.6% and 23.3% variations, respectively. Based on the rankings of genotypes, G37 (ICPL 20205), G35 (ICPL 20203), G8 (ICPL 19404), G17 (ICPL 19415), and G9 (ICPL 19405) were identified as ideal genotypes. Discriminativeness vs. representativeness identified GKVK Bengaluru as an ideal environment for comprehensive evaluation of test genotypes. However, ICPL 19405 was identified as the potentially stable high-yielding genotype for further testing and release across the test environments based on its mean grain yield (1,469.30 kg/ha), least ASV (3.82), and low yield stability index (YSI) of 13.
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Kandarkar K, Palaniappan V, Satpathy S, Vemula A, Rajasekaran R, Jeyakumar P, Sevugaperumal N, Gupta SK. Understanding genetic diversity in drought-adaptive hybrid parental lines in pearl millet. PLoS One 2024; 19:e0298636. [PMID: 38394324 PMCID: PMC10890771 DOI: 10.1371/journal.pone.0298636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 01/27/2024] [Indexed: 02/25/2024] Open
Abstract
Information on genetic diversity and population structure is helpful to strategize enhancing the genetic base of hybrid parental lines in breeding programs. The present study determined the population structure and genetic diversity of 109 pearl millet hybrid parental lines, known for their better adaptation and performance in drought-prone environments, using 16,472 single nucleotide polymorphic (SNP) markers generated from GBS (genotyping-by-sequencing) platforms. The SNPs were distributed uniformly across the pearl millet genome and showed considerable genetic diversity (0.337), expected heterozygosity (0.334), and observed heterozygosity (0.031). Most of the pairs of lines (78.36%) had Identity-by-State (IBS) based genetic distances of more than 0.3, indicating a significant amount of genetic diversity among the parental lines. Bayesian model-based population stratification, neighbor-joining phylogenetic analysis, and principal coordinate analysis (PCoA) differentiated all hybrid parental lines into two clear-cut major groups, one each for seed parents (B-lines) and pollinators (R-lines). Majority of parental lines sharing common parentages were found grouped in the same cluster. Analysis of molecular variance (AMOVA) revealed 7% of the variation among subpopulations, and 93% of the variation was attributable to within sub-populations. Chromosome 3 had the highest number of LD regions. Genomic LD decay distance was 0.69 Mb and varied across the different chromosomes. Genetic diversity based on 11 agro-morphological and grain quality traits also suggested that the majority of the B- and R-lines were grouped into two major clusters with few overlaps. In addition, the combined analysis of phenotypic and genotypic data showed similarities in the population grouping patterns. The present study revealed the uniqueness of most of the inbred lines, which can be a valuable source of new alleles and help breeders to utilize these inbred lines for the development of hybrids in drought-prone environments.
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Somegowda VK, Prasad KVSV, Naravula J, Vemula A, Selvanayagam S, Rathore A, Jones CS, Gupta R, Deshpande SP. Genetic Dissection and Quantitative Trait Loci Mapping of Agronomic and Fodder Quality Traits in Sorghum Under Different Water Regimes. FRONTIERS IN PLANT SCIENCE 2022; 13:810632. [PMID: 35251083 PMCID: PMC8892184 DOI: 10.3389/fpls.2022.810632] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 01/03/2022] [Indexed: 06/01/2023]
Abstract
Livestock provides an additional source of income for marginal cropping farmers, but crop residues that are used as a main source of animal feed are characteristically low in digestibility and protein content. This reduces the potential livestock product yield and quality. The key trait, which influences the quality and the cost of animal feed, is digestibility. In this study, we demonstrate that sorghum breeding can be directed to achieve genetic gains for both fodder biomass and digestibility without any trade-offs. The genotypic variance has shown significant differences for biomass across years (13,035 in 2016 and 3,395 in 2017) while in vitro organic matter digestibility (IVOMD) showed significant genotypic variation in 2016 (0.253) under drought. A range of agronomic and fodder quality traits was found to vary significantly in the population within both the control and drought conditions and across both years of the study. There was significant genotypic variance (σg2) and genotypic × treatment variance (σgxt2) in dry matter production in a recombinant inbred line (RIL) population in both study years, while there was only significant σg2 and σgxt2 in IVOMD under the control conditions. There was no significant correlation identified between biomass and digestibility traits under the control conditions, but there was a positive correlation under drought. However, a negative relation was observed between digestibility and grain yield under the control conditions, while there was no significant correlation under drought population, which was genotyped using the genotyping-by-sequencing (GBS) technique, and 1,141 informative single nucleotide polymorphism (SNP) markers were identified. A linkage map was constructed, and a total of 294 quantitative trait loci (QTLs) were detected, with 534 epistatic interactions, across all of the traits under study. QTL for the agronomic traits fresh and dry weight, together with plant height, mapped on to the linkage group (LG) 7, while QTL for IVOMD mapped on to LG1, 2, and 8. A number of genes previously reported to play a role in nitrogen metabolism and cell wall-related functions were found to be associated with these QTL.
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Palakurthi R, Jayalakshmi V, Kumar Y, Kulwal P, Yasin M, Kute NS, Laxuman C, Yeri S, Vemula A, Rathore A, Samineni S, Soren KR, Mondal B, Dixit GP, Bharadwaj C, Chaturvedi SK, Gaur PM, Roorkiwal M, Thudi M, Singh NP, Varshney RK. Translational Chickpea Genomics Consortium to Accelerate Genetic Gains in Chickpea (Cicer arietinum L.). PLANTS 2021; 10:plants10122583. [PMID: 34961053 PMCID: PMC8703834 DOI: 10.3390/plants10122583] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/23/2021] [Accepted: 10/30/2021] [Indexed: 12/03/2022]
Abstract
The Translational Chickpea Genomics Consortium (TCGC) was set up to increase the production and productivity of chickpea (Cicer arietinum L.). It represents research institutes from six major chickpea growing states (Madhya Pradesh, Maharashtra, Andhra Pradesh, Telangana, Karnataka and Uttar Pradesh) of India. The TCGC team has been engaged in deploying modern genomics approaches in breeding and popularizing improved varieties in farmers’ fields across the states. Using marker-assisted backcrossing, introgression lines with enhanced drought tolerance and fusarium wilt resistance have been developed in the genetic background of 10 elite varieties of chickpea. Multi-location evaluation of 100 improved lines (70 desi and 30 kabuli) during 2016–2017 and 2018–2019 enabled the identification of top performing desi and kabuli lines. In total, 909 Farmer Participatory Varietal Selection trials were conducted in 158 villages in 16 districts of the five states, during 2017–2018, 2018–2019, and 2019–2020, involving 16 improved varieties. New molecular breeding lines developed in different genetic backgrounds are potential candidates for national trials under the ICAR-All India Coordinated Research Project on Chickpea. The comprehensive efforts of TCGC resulted in the development and adoption of high-yielding varieties that will increase chickpea productivity and the profitability of chickpea growing farmers.
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Bollam S, Romana KK, Rayaprolu L, Vemula A, Das RR, Rathore A, Gandham P, Chander G, Deshpande SP, Gupta R. Nitrogen Use Efficiency in Sorghum: Exploring Native Variability for Traits Under Variable N-Regimes. FRONTIERS IN PLANT SCIENCE 2021; 12:643192. [PMID: 33968102 PMCID: PMC8097177 DOI: 10.3389/fpls.2021.643192] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/29/2021] [Indexed: 06/12/2023]
Abstract
Exploring the natural genetic variability and its exploitation for improved Nitrogen Use Efficiency (NUE) in sorghum is one of the primary goals in the modern crop improvement programs. The integrated strategies include high-throughput phenotyping, next generation sequencing (NGS)-based genotyping technologies, and a priori selected candidate gene studies that help understand the detailed physiological and molecular mechanisms underpinning this complex trait. A set of sixty diverse sorghum genotypes was evaluated for different vegetative, reproductive, and yield traits related to NUE in the field (under three N regimes) for two seasons. Significant variations for different yield and related traits under 0 and 50% N confirmed the availability of native genetic variability in sorghum under low N regimes. Sorghum genotypes with distinct genetic background had interestingly similar NUE associated traits. The Genotyping-By-Sequencing based SNPs (>89 K) were used to study the population structure, and phylogenetic groupings identified three distinct groups. The information of grain N and stalk N content of the individuals covered on the phylogenetic groups indicated randomness in the distribution for adaptation under variable N regimes. This study identified promising sorghum genotypes with consistent performance under varying environments, with buffer capacity for yield under low N conditions. We also report better performing genotypes for varied production use-grain, stover, and dual-purpose sorghum having differential adaptation response to NUE traits. Expression profiling of NUE associated genes in shoot and root tissues of contrasting lines (PVK801 and HDW703) grown in varying N conditions revealed interesting outcomes. Root tissues of contrasting lines exhibited differential expression profiles for transporter genes [ammonium transporter (SbAMT), nitrate transporters (SbNRT)]; primary assimilatory (glutamine synthetase (SbGS), glutamate synthase (SbGOGAT[NADH], SbGOGAT[Fd]), assimilatory genes [nitrite reductase (SbNiR[NADH]3)]; and amino acid biosynthesis associated gene [glutamate dehydrogenase (SbGDH)]. Identification and expression profiling of contrasting sorghum genotypes in varying N dosages will provide new information to understand the response of NUE genes toward adaptation to the differential N regimes in sorghum. High NUE genotypes identified from this study could be potential candidates for in-depth molecular analysis and contribute toward the development of N efficient sorghum cultivars.
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Bharadwaj C, Tripathi S, Soren KR, Thudi M, Singh RK, Sheoran S, Roorkiwal M, Patil BS, Chitikineni A, Palakurthi R, Vemula A, Rathore A, Kumar Y, Chaturvedi SK, Mondal B, Shanmugavadivel PS, Srivastava AK, Dixit GP, Singh NP, Varshney RK. Introgression of "QTL-hotspot" region enhances drought tolerance and grain yield in three elite chickpea cultivars. THE PLANT GENOME 2021; 14:e20076. [PMID: 33480153 DOI: 10.1002/tpg2.20076] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 11/10/2020] [Indexed: 05/27/2023]
Abstract
With an aim of enhancing drought tolerance using a marker-assisted backcrossing (MABC) approach, we introgressed the "QTL-hotspot" region from ICC 4958 accession that harbors quantitative trait loci (QTLs) for several drought-tolerance related traits into three elite Indian chickpea (Cicer arietinum L.) cultivars: Pusa 372, Pusa 362, and DCP 92-3. Of eight simple sequence repeat (SSR) markers in the QTL-hotspot region, two to three polymorphic markers were used for foreground selection with respective cross-combinations. A total of 47, 53, and 46 SSRs were used for background selection in case of introgression lines (ILs) developed in genetic backgrounds of Pusa 372, Pusa 362, and DCP 92-3, respectively. In total, 61 ILs (20 BC3 F3 in Pusa 372; 20 BC2 F3 in Pusa 362, and 21 BC3 F3 in DCP 92-3), with >90% recurrent parent genome recovery were developed. Six improved lines in different genetic backgrounds (e.g. BGM 10216 in Pusa 372; BG 3097 and BG 4005 in Pusa 362; IPC(L4-14), IPC(L4-16), and IPC(L19-1) in DCP 92-3) showed better performance than their respective recurrent parents. BGM 10216, with 16% yield gain over Pusa 372, has been released as Pusa Chickpea 10216 by the Central Sub-Committees on Crop Standards, Notification and Release of Varieties of Agricultural Crops, Ministry of Agriculture and Farmers Welfare, Government of India, for commercial cultivation in India. In summary, this study reports introgression of the QTL-hotspot for enhancing yield under rainfed conditions, development of several introgression lines, and release of Pusa Chickpea 10216 developed through molecular breeding in India.
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Pandey SK, Dasgupta T, Rathore A, Vemula A. Relationship of Parental Genetic Distance with Heterosis and Specific Combining Ability in Sesame (Sesamum indicum L.) Based on Phenotypic and Molecular Marker Analysis. Biochem Genet 2018; 56:188-209. [PMID: 29322371 DOI: 10.1007/s10528-017-9837-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 12/29/2017] [Indexed: 11/30/2022]
Abstract
The genetic distance analysis for selection of suitable parents has been established and effectively used in many crops; however, there is dearth of conclusive report of relationship of genetic distance analysis with heterosis in sesame. In the present study, an attempt was made to estimate the associations of genetic distances using SSR (GDSSR), seed-storage protein profiling (GDSDS) and agro-morphological traits (GDMOR) with hybrid performance. Seven parents were selected from 60 exotic and Indian genotypes based on genetic distance from clustering pattern based on SSR, seed-storage protein, morphological traits and per se performance. For combining ability analysis, 7 parents and 21 crosses generated from 7 × 7 half diallel evaluated at two environments in a replicated field trial during pre-kharif season of 2013. Compared with the average parents yield (12.57 g plant-1), eight hybrids had a significant (P < 0.01) yield advantage across environments, with averages of 26.94 and 29.99% for better-parent heterosis (BPH) and mid-parent heterosis (MPH), respectively, across environments. Highly significant positive correlation was observed between specific combining ability (SCA) and per se performance (0.97), while positive non-significant correlation of BPH with GDSSR (0.048), and non-significant negative correlations with GDMOR (- 0.01) and GDSDS (- 0.256) were observed. The linear regressions of SCA on MPH, BPH and per se performance of F1s were significant with R2 value of 0.88, 0.84 and 0.95 respectively. The present findings revealed a weak association of GDSSR with F1's performance; however, SCA has appeared as an important factor in the determination of heterosis and per se performance of the hybrids. The present findings also indicated that parental divergence in the intermediate group would likely produce high heterotic crosses in sesame.
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Varshney RK, Thudi M, Nayak SN, Gaur PM, Kashiwagi J, Krishnamurthy L, Jaganathan D, Koppolu J, Bohra A, Tripathi S, Rathore A, Jukanti AK, Jayalakshmi V, Vemula A, Singh SJ, Yasin M, Sheshshayee MS, Viswanatha KP. Genetic dissection of drought tolerance in chickpea (Cicer arietinum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:445-62. [PMID: 24326458 PMCID: PMC3910274 DOI: 10.1007/s00122-013-2230-6] [Citation(s) in RCA: 176] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 10/31/2013] [Indexed: 05/19/2023]
Abstract
Analysis of phenotypic data for 20 drought tolerance traits in 1-7 seasons at 1-5 locations together with genetic mapping data for two mapping populations provided 9 QTL clusters of which one present on CaLG04 has a high potential to enhance drought tolerance in chickpea improvement. Chickpea (Cicer arietinum L.) is the second most important grain legume cultivated by resource poor farmers in the arid and semi-arid regions of the world. Drought is one of the major constraints leading up to 50% production losses in chickpea. In order to dissect the complex nature of drought tolerance and to use genomics tools for enhancing yield of chickpea under drought conditions, two mapping populations-ICCRIL03 (ICC 4958 × ICC 1882) and ICCRIL04 (ICC 283 × ICC 8261) segregating for drought tolerance-related root traits were phenotyped for a total of 20 drought component traits in 1-7 seasons at 1-5 locations in India. Individual genetic maps comprising 241 loci and 168 loci for ICCRIL03 and ICCRIL04, respectively, and a consensus genetic map comprising 352 loci were constructed ( http://cmap.icrisat.ac.in/cmap/sm/cp/varshney/). Analysis of extensive genotypic and precise phenotypic data revealed 45 robust main-effect QTLs (M-QTLs) explaining up to 58.20% phenotypic variation and 973 epistatic QTLs (E-QTLs) explaining up to 92.19% phenotypic variation for several target traits. Nine QTL clusters containing QTLs for several drought tolerance traits have been identified that can be targeted for molecular breeding. Among these clusters, one cluster harboring 48% robust M-QTLs for 12 traits and explaining about 58.20% phenotypic variation present on CaLG04 has been referred as "QTL-hotspot". This genomic region contains seven SSR markers (ICCM0249, NCPGR127, TAA170, NCPGR21, TR11, GA24 and STMS11). Introgression of this region into elite cultivars is expected to enhance drought tolerance in chickpea.
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