Identification of genomic regions associated with early plant vigour in lentil (Lens culinaris)

Mane, Rushikesh; Katoch, Megha; Singh, Maneet; Sharma, R. A.; Sharma, T. R.; Chahota, Rakesh Kumar

doi:10.1007/s12041-020-1182-2

Cited by 7 publications

(5 citation statements)

References 61 publications

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“…More recently, 433 SSRs from the lentil genome, 145 SSRs from other legumes, 25 ISSR, and 250 RAPD markers have been used for the development of a linkage map consisting of 265 markers. These markers were assigned on seven LGs with a total genetic distance of 809.4 cM with an average marker density of 3.05 cM (Mane et al, 2020). Further reduction in the cost of sequencing has led to the development of a greater number of high‐density linkage maps based only on SNP markers in lentil (Aldemir et al, 2017; Bhadauria, Ramsay, et al, 2017; Gujarai‐Verma et al, 2014; Ma et al, 2020; Polanco et al, 2019; Sudheesh, Rodda, et al, 2016; Temel et al, 2014).…”

Section: Acceleration In the Development Of Genomic Resources For Elevating Lentil From Orphan Statusmentioning

confidence: 99%

Genomics‐assisted lentil breeding: Current status and future strategies

et al. 2021

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Genomics‐assisted breeding has become a powerful tool to develop high‐yielding climate‐resilient varieties for adaptation to adverse environmental conditions such as heat and drought stresses. Previously, efforts have been made to develop genomic resources in lentil, leading to the development of many trait‐specific mapping populations, cores and mini‐cores, and single nucleotide polymorphism and simple sequence repeat markers. Molecular markers have been used in genetic diversity analyses and to clarify genetic relationships in lentil. However, availability of cost‐effective next‐generation sequencing and genotyping‐by‐sequencing technologies has provided unprecedented opportunities for advancing genetics research and breeding applications. For instance, it has become possible to assemble the large and complex genome, develop high‐density genetic maps for high‐resolution QTL mapping, and deploy genome‐wide association study in lentil. Furthermore, a range of cost‐effective marker genotyping platforms have been developed. These developments offer ample opportunities to modernize current breeding programs in lentil for accelerating genetic gains. This review discusses the current status and future possibilities of genomics‐assisted breeding to develop and deploy lentil cultivars suitable for changing climatic conditions.

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Section: Acceleration In the Development Of Genomic Resources For Elevating Lentil From Orphan Statusmentioning

confidence: 99%

Genomics‐assisted lentil breeding: Current status and future strategies

et al. 2021

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“…Genetic mapping studies have helped in identifying many genes and QTLs controlling abiotic and biotic stress tolerance, growth, development and nutritional parameters have been mapped in lentil ( Eujayl et al., 1998 ; Tullu et al., 2003 ; Tullu et al., 2006b ; Durán et al., 2004 ; Kahraman et al., 2004 ; Hamwieh et al., 2005 ; Gupta et al., 2012a ; Saha et al., 2013 ; Kaur et al., 2014 ; Ates et al., 2016 ; Idrissi et al., 2016 ; Sudheesh et al., 2016 ; Rodda et al., 2017 ; Ates et al., 2018 ; Polanco et al., 2019 ; Ma et al., 2020 ; Mane et al., 2020 ; Gela et al., 2021a, b ). The details about genetic linkage maps constructed with QTLs governing the traits of interest have been listed in Table 3 .…”

Section: Qtl and Association Mappingmentioning

confidence: 99%

“…The mapping population was a cross between accessions ‘IPL 220 and ILWL 118’ of wild species L. orientalis ( Kumar et al., 2019 ). A QTL hotspot was observed consisting of six QTLs for lengths of root, shoot and seedling within a map distances of 56.61-86.81 cM range on LG1 using F 10 RIL population of cross ‘WA8649090 x Precoz’ ( Mane et al., 2020 ). Likewise, a total of 143 accessions were analysed by GWAS to establish associations between prebiotic carbohydrates and candidate genes ( Johnson et al., 2021 ).…”

Section: Qtl and Association Mappingmentioning

confidence: 99%

The Prospects of gene introgression from crop wild relatives into cultivated lentil for climate change mitigation

et al. 2023

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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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“…In addition, QTL mapping has been used to map genomic regions associated with plant development, abiotic stress tolerance, disease resistance, and nutritional parameters. Mane et al (2020) identified few QTLs from RIL populations of a cross between WA8649090 × Precoz ( Table 1 ). The QTLs were related to plant developmental processes, such as a QTL-hotspot representing six QTLs for shoot length, root length, and seedling length.…”

Section: Genomic Innovations Reveal a New Genetic Landscape For Lenti...mentioning

confidence: 99%

Omics Path to Increasing Productivity in Less-Studied Crops Under Changing Climate—Lentil a Case Study

et al. 2022

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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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Identification of genomic regions associated with early plant vigour in lentil (Lens culinaris)

Cited by 7 publications

References 61 publications

Genomics‐assisted lentil breeding: Current status and future strategies

Genomics‐assisted lentil breeding: Current status and future strategies

The Prospects of gene introgression from crop wild relatives into cultivated lentil for climate change mitigation

Omics Path to Increasing Productivity in Less-Studied Crops Under Changing Climate—Lentil a Case Study

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