Superior haplotypes for haplotype‐based breeding for drought tolerance in pigeonpea (<i>Cajanus cajan</i> L.)

Sinha, Pallavi; Singh, Vikas K.; Saxena, Rachit K.; Khan, Aamir W.; Abbai, Ragavendran; Chitikineni, Annapurna; Desai, Aarthi; Molla, Johiruddin; Upadhyaya, Hari D.; Kumar, Arvind; Varshney, Rajeev K.

doi:10.1111/pbi.13422

Cited by 84 publications

(47 citation statements)

References 27 publications

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“…We believe that one or a combination of the following three genomic breeding approaches, namely MAS/MABC, haplotype-based breeding (HBB) and genomic prediction, can be used to develop superior lines. While MAS/MABC has been successfully used for product development, HBB has shown huge potential for trait improvement in rice ( Abbai et al, 2019 ) and pigeonpea ( Sinha et al, 2020 ). During recent years the accuracy and prediction of predicting phenotypes in genomics selection has been improved extensively through approaches including (i) estimating global GEBVs while considering interaction of marker and environment covariates (G × E) ( Jarquín et al, 2014 ; Crossa et al, 2017 ), (ii) estimating haplotype/bin- based local GEBVs ( Voss-Fels et al, 2019 ), (iii) WhoGEM approach that explores the relationships between phenotypes and admixture components, land types, admixture components × environment interactions, and controls for the environment ( Gentzbittel et al, 2019 ), and (iv) optimal contribution selection method that enables simultaneous trait improvement and enriching the genetic base ( Woolliams et al, 2015 ; Cowling et al, 2017 ).…”

Section: Future Perspectivesmentioning

confidence: 99%

Genomic resources in plant breeding for sustainable agriculture

Thudi

Ramesh

Schnable

et al. 2021

Journal of Plant Physiology

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121

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Climate change during the last 40 years has had a serious impact on agriculture and threatens global food and nutritional security. From over half a million plant species, cereals and legumes are the most important for food and nutritional security. Although systematic plant breeding has a relatively short history, conventional breeding coupled with advances in technology and crop management strategies has increased crop yields by 56 % globally between 1965−85, referred to as the Green Revolution. Nevertheless, increased demand for food, feed, fiber, and fuel necessitates the need to break existing yield barriers in many crop plants. In the first decade of the 21st century we witnessed rapid discovery, transformative technological development and declining costs of genomics technologies. In the second decade, the field turned towards making sense of the vast amount of genomic information and subsequently moved towards accurately predicting gene-to-phenotype associations and tailoring plants for climate resilience and global food security. In this review we focus on genomic resources, genome and germplasm sequencing, sequencing-based trait mapping, and genomics-assisted breeding approaches aimed at developing biotic stress resistant, abiotic stress tolerant and high nutrition varieties in six major cereals (rice, maize, wheat, barley, sorghum and pearl millet), and six major legumes (soybean, groundnut, cowpea, common bean, chickpea and pigeonpea). We further provide a perspective and way forward to use genomic breeding approaches including marker-assisted selection, marker-assisted backcrossing, haplotype based breeding and genomic prediction approaches coupled with machine learning and artificial intelligence, to speed breeding approaches. The overall goal is to accelerate genetic gains and deliver climate resilient and high nutrition crop varieties for sustainable agriculture.

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Section: Future Perspectivesmentioning

confidence: 99%

Genomic resources in plant breeding for sustainable agriculture

Thudi

Ramesh

Schnable

et al. 2021

Journal of Plant Physiology

Self Cite

121

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“…Retrospectively, targeted analysis of superior haplotypes across mega-varieties may help revealing combinations of superior haplotypes that explain the genetic basis of the highperformance of these lines. In pigeonpea, Sinha et al (2020) found complete absence of superior haplotypes for drought tolerance in popular varieties Maruti (ICP 8863) and Jagriti (ICPL 151), thus offering possibilities for further improvement of such high-yielding varieties. In parallel, increasing sequencing data on wild relatives will aid in the discovery of new haplotypes that the cultivated pool currently lacks.…”

Section: Haplotype-based Breedingmentioning

confidence: 99%

“…As has been demonstrated in rice, a panel of sequenced lines capturing the maximum diversity is deemed suitable for phenotypic validation of haplotypes defining key traits (Abbai et al ., 2019). A similar haplo‐pheno analysis in pigeonpea validated superior haplotypes of three genes for drought tolerance that were identified by mining of the WGRS data set and candidate gene‐based association analysis (Sinha et al ., 2020). The study also identified a set of promising lines carrying these superior haplotypes.…”

Section: Breeding Strategies To Deliver Higher Genetic Gainsmentioning

confidence: 99%

“…The study also identified a set of promising lines carrying these superior haplotypes. Introgression of superior haplotypes in breeding has been referred as haplotype‐based breeding (Sinha et al ., 2020; Varshney et al ., 2020).…”

Section: Breeding Strategies To Deliver Higher Genetic Gainsmentioning

confidence: 99%

“…In pigeonpea, Sinha et al . (2020) found complete absence of superior haplotypes for drought tolerance in popular varieties Maruti (ICP 8863) and Jagriti (ICPL 151), thus offering possibilities for further improvement of such high‐yielding varieties. In parallel, increasing sequencing data on wild relatives will aid in the discovery of new haplotypes that the cultivated pool currently lacks.…”

Section: Breeding Strategies To Deliver Higher Genetic Gainsmentioning

confidence: 99%

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Genomic interventions for sustainable agriculture

Bohra

Jha

Godwin

et al. 2020

Plant Biotechnology Journal

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Agricultural production faces a Herculean challenge to feed the increasing global population. Food production systems need to deliver more with finite land and water resources while exerting the least negative influence on the ecosystem. The unpredictability of climate change and consequent changes in pests/pathogens dynamics aggravate the enormity of the challenge. Crop improvement has made significant contributions towards food security, and breeding climate-smart cultivars are considered the most sustainable way to accelerate food production. However, a fundamental change is needed in the conventional breeding framework in order to respond adequately to the growing food demands. Progress in genomics has provided new concepts and tools that hold promise to make plant breeding procedures more precise and efficient. For instance, reference genome assemblies in combination with germplasm sequencing delineate breeding targets that could contribute to securing future food supply. In this review, we highlight key breakthroughs in plant genome sequencing and explain how the presence of these genome resources in combination with gene editing techniques has revolutionized the procedures of trait discovery and manipulation. Adoption of new approaches such as speed breeding, genomic selection and haplotype-based breeding could overcome several limitations of conventional breeding. We advocate that strengthening varietal release and seed distribution systems will play a more determining role in delivering genetic gains at farmer's field. A holistic approach outlined here would be crucial to deliver steady stream of climate-smart crop cultivars for sustainable agriculture.

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