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Balech R, Maalouf F, Kaur S, Jighly A, Joukhadar R, Alsamman AM, Hamwieh A, Khater LA, Rubiales D, Kumar S. Identification of novel genes associated with herbicide tolerance in Lentil (Lens culinaris ssp. culinaris Medik.). Sci Rep 2024; 14:10215. [PMID: 38702403 PMCID: PMC11068770 DOI: 10.1038/s41598-024-59695-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 04/15/2024] [Indexed: 05/06/2024] Open
Abstract
Weeds pose a major constraint in lentil cultivation, leading to decrease farmers' revenues by reducing the yield and increasing the management costs. The development of herbicide tolerant cultivars is essential to increase lentil yield. Even though herbicide tolerant lines have been identified in lentils, breeding efforts are still limited and lack proper validation. Marker assisted selection (MAS) can increase selection accuracy at early generations. Total 292 lentil accessions were evaluated under different dosages of two herbicides, metribuzin and imazethapyr, during two seasons at Marchouch, Morocco and Terbol, Lebanon. Highly significant differences among accessions were observed for days to flowering (DF) and maturity (DM), plant height (PH), biological yield (BY), seed yield (SY), number of pods per plant (NP), as well as the reduction indices (RI) for PH, BY, SY and NP. A total of 10,271 SNPs markers uniformly distributed along the lentil genome were assayed using Multispecies Pulse SNP chip developed at Agriculture Victoria, Melbourne. Meta-GWAS analysis was used to detect marker-trait associations, which detected 125 SNPs markers associated with different traits and clustered in 85 unique quantitative trait loci. These findings provide valuable insights for initiating MAS programs aiming to enhance herbicide tolerance in lentil crop.
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Affiliation(s)
- Rind Balech
- International Center for Agricultural Research in the Dry Areas (ICARDA), Terbol, Lebanon.
| | - Fouad Maalouf
- International Center for Agricultural Research in the Dry Areas (ICARDA), Terbol, Lebanon.
| | - Sukhjiwan Kaur
- Department of Energy, AgriBio, Environment and Climate Action, Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC, 3083, Australia
| | - Abdulqader Jighly
- Department of Energy, AgriBio, Environment and Climate Action, Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC, 3083, Australia
| | - Reem Joukhadar
- Department of Energy, AgriBio, Environment and Climate Action, Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC, 3083, Australia
| | | | | | - Lynn Abou Khater
- International Center for Agricultural Research in the Dry Areas (ICARDA), Terbol, Lebanon
| | - Diego Rubiales
- Institute for Sustainable Agriculture, CSIC, Córdoba, Spain
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Susmitha P, Kumar P, Yadav P, Sahoo S, Kaur G, Pandey MK, Singh V, Tseng TM, Gangurde SS. Genome-wide association study as a powerful tool for dissecting competitive traits in legumes. FRONTIERS IN PLANT SCIENCE 2023; 14:1123631. [PMID: 37645459 PMCID: PMC10461012 DOI: 10.3389/fpls.2023.1123631] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 06/08/2023] [Indexed: 08/31/2023]
Abstract
Legumes are extremely valuable because of their high protein content and several other nutritional components. The major challenge lies in maintaining the quantity and quality of protein and other nutritional compounds in view of climate change conditions. The global need for plant-based proteins has increased the demand for seeds with a high protein content that includes essential amino acids. Genome-wide association studies (GWAS) have evolved as a standard approach in agricultural genetics for examining such intricate characters. Recent development in machine learning methods shows promising applications for dimensionality reduction, which is a major challenge in GWAS. With the advancement in biotechnology, sequencing, and bioinformatics tools, estimation of linkage disequilibrium (LD) based associations between a genome-wide collection of single-nucleotide polymorphisms (SNPs) and desired phenotypic traits has become accessible. The markers from GWAS could be utilized for genomic selection (GS) to predict superior lines by calculating genomic estimated breeding values (GEBVs). For prediction accuracy, an assortment of statistical models could be utilized, such as ridge regression best linear unbiased prediction (rrBLUP), genomic best linear unbiased predictor (gBLUP), Bayesian, and random forest (RF). Both naturally diverse germplasm panels and family-based breeding populations can be used for association mapping based on the nature of the breeding system (inbred or outbred) in the plant species. MAGIC, MCILs, RIAILs, NAM, and ROAM are being used for association mapping in several crops. Several modifications of NAM, such as doubled haploid NAM (DH-NAM), backcross NAM (BC-NAM), and advanced backcross NAM (AB-NAM), have also been used in crops like rice, wheat, maize, barley mustard, etc. for reliable marker-trait associations (MTAs), phenotyping accuracy is equally important as genotyping. Highthroughput genotyping, phenomics, and computational techniques have advanced during the past few years, making it possible to explore such enormous datasets. Each population has unique virtues and flaws at the genomics and phenomics levels, which will be covered in more detail in this review study. The current investigation includes utilizing elite breeding lines as association mapping population, optimizing the choice of GWAS selection, population size, and hurdles in phenotyping, and statistical methods which will analyze competitive traits in legume breeding.
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Affiliation(s)
- Pusarla Susmitha
- Regional Agricultural Research Station, Acharya N.G. Ranga Agricultural University, Andhra Pradesh, India
| | - Pawan Kumar
- Department of Genetics and Plant Breeding, College of Agriculture, Chaudhary Charan Singh (CCS) Haryana Agricultural University, Hisar, India
| | - Pankaj Yadav
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Rajasthan, India
| | - Smrutishree Sahoo
- Department of Genetics and Plant Breeding, School of Agriculture, Gandhi Institute of Engineering and Technology (GIET) University, Odisha, India
| | - Gurleen Kaur
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Manish K. Pandey
- Department of Genomics, Prebreeding and Bioinformatics, International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Varsha Singh
- Department of Plant and Soil Sciences, Mississippi State University, Starkville, MS, United States
| | - Te Ming Tseng
- Department of Plant and Soil Sciences, Mississippi State University, Starkville, MS, United States
| | - Sunil S. Gangurde
- Department of Plant Pathology, University of Georgia, Tifton, GA, United States
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Rajpal VR, Singh A, Kathpalia R, Thakur RK, Khan MK, Pandey A, Hamurcu M, Raina SN. The Prospects of gene introgression from crop wild relatives into cultivated lentil for climate change mitigation. FRONTIERS IN PLANT SCIENCE 2023; 14:1127239. [PMID: 36998696 PMCID: PMC10044020 DOI: 10.3389/fpls.2023.1127239] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 02/22/2023] [Indexed: 05/31/2023]
Abstract
Crop wild relatives (CWRs), landraces and exotic germplasm are important sources of genetic variability, alien alleles, and useful crop traits that can help mitigate a plethora of abiotic and biotic stresses and crop yield reduction arising due to global climatic changes. In the pulse crop genus Lens, the cultivated varieties have a narrow genetic base due to recurrent selections, genetic bottleneck and linkage drag. The collection and characterization of wild Lens germplasm resources have offered new avenues for the genetic improvement and development of stress-tolerant, climate-resilient lentil varieties with sustainable yield gains to meet future food and nutritional requirements. Most of the lentil breeding traits such as high-yield, adaptation to abiotic stresses and resistance to diseases are quantitative and require the identification of quantitative trait loci (QTLs) for marker assisted selection and breeding. Advances in genetic diversity studies, genome mapping and advanced high-throughput sequencing technologies have helped identify many stress-responsive adaptive genes, quantitative trait loci (QTLs) and other useful crop traits in the CWRs. The recent integration of genomics technologies with plant breeding has resulted in the generation of dense genomic linkage maps, massive global genotyping, large transcriptomic datasets, single nucleotide polymorphisms (SNPs), expressed sequence tags (ESTs) that have advanced lentil genomic research substantially and allowed for the identification of QTLs for marker-assisted selection (MAS) and breeding. Assembly of lentil and its wild species genomes (~4Gbp) opens up newer possibilities for understanding genomic architecture and evolution of this important legume crop. This review highlights the recent strides in the characterization of wild genetic resources for useful alleles, development of high-density genetic maps, high-resolution QTL mapping, genome-wide studies, MAS, genomic selections, new databases and genome assemblies in traditionally bred genus Lens for future crop improvement amidst the impending global climate change.
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Affiliation(s)
- Vijay Rani Rajpal
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
| | - Apekshita Singh
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Sector 125, Noida, U.P., India
| | - Renu Kathpalia
- Department of Botany, Kirori Mal College, University of Delhi, Delhi, India
| | - Rakesh Kr. Thakur
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Sector 125, Noida, U.P., India
| | - Mohd. Kamran Khan
- Department of Soil Science and Plant Nutrition, Faculty of Agriculture, Selcuk University, Konya, Türkiye
| | - Anamika Pandey
- Department of Soil Science and Plant Nutrition, Faculty of Agriculture, Selcuk University, Konya, Türkiye
| | - Mehmet Hamurcu
- Department of Soil Science and Plant Nutrition, Faculty of Agriculture, Selcuk University, Konya, Türkiye
| | - Soom Nath Raina
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Sector 125, Noida, U.P., India
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Tiwari M, Singh B, Min D, Jagadish SVK. Omics Path to Increasing Productivity in Less-Studied Crops Under Changing Climate-Lentil a Case Study. FRONTIERS IN PLANT SCIENCE 2022; 13:813985. [PMID: 35615121 PMCID: PMC9125188 DOI: 10.3389/fpls.2022.813985] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 04/04/2022] [Indexed: 05/08/2023]
Abstract
Conventional breeding techniques for crop improvement have reached their full potential, and hence, alternative routes are required to ensure a sustained genetic gain in lentils. Although high-throughput omics technologies have been effectively employed in major crops, less-studied crops such as lentils have primarily relied on conventional breeding. Application of genomics and transcriptomics in lentils has resulted in linkage maps and identification of QTLs and candidate genes related to agronomically relevant traits and biotic and abiotic stress tolerance. Next-generation sequencing (NGS) complemented with high-throughput phenotyping (HTP) technologies is shown to provide new opportunities to identify genomic regions and marker-trait associations to increase lentil breeding efficiency. Recent introduction of image-based phenotyping has facilitated to discern lentil responses undergoing biotic and abiotic stresses. In lentil, proteomics has been performed using conventional methods such as 2-D gel electrophoresis, leading to the identification of seed-specific proteome. Metabolomic studies have led to identifying key metabolites that help differentiate genotypic responses to drought and salinity stresses. Independent analysis of differentially expressed genes from publicly available transcriptomic studies in lentils identified 329 common transcripts between heat and biotic stresses. Similarly, 19 metabolites were common across legumes, while 31 were common in genotypes exposed to drought and salinity stress. These common but differentially expressed genes/proteins/metabolites provide the starting point for developing high-yielding multi-stress-tolerant lentils. Finally, the review summarizes the current findings from omic studies in lentils and provides directions for integrating these findings into a systems approach to increase lentil productivity and enhance resilience to biotic and abiotic stresses under changing climate.
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Affiliation(s)
- Manish Tiwari
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
- *Correspondence: Manish Tiwari,
| | - Baljinder Singh
- National Institute of Plant Genome Research, New Delhi, India
| | - Doohong Min
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
| | - S. V. Krishna Jagadish
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
- S. V. Krishna Jagadish,
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