Features and applications of haplotypes in crop breeding

Bhat, Javaid Akhter; Yu, Deyue; Bohra, Abhishek; Ganie, Showkat Ahmad; Varshney, Rajeev K.

doi:10.1038/s42003-021-02782-y

Cited by 93 publications

(80 citation statements)

References 158 publications

(187 reference statements)

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“…In addition to GS, modern and innovative plant-breeding methods such as speed breeding [157,158], doubled haploid-based breeding (DHB) [159], haplotype-based breeding [160], fast forward breeding [161], and genome-editing-based breeding [162] approaches can be harnessed in RSHS tolerance breeding. Speed breeding (SB) technology encompasses growing plant populations under controlled environments such as glasshouses and growth chambers to shorten the breeding cycles and accelerates crop research via rapid generation advancement, for instance, via single-seed descent (SSD), and can potentially be deployed to large-scale crop breeding programs [158].…”

Section: Genomic Selection and Modern Plant-breeding Methodsmentioning

confidence: 99%

Reproductive-Stage Heat Stress in Cereals: Impact, Plant Responses and Strategies for Tolerance Improvement

Zenda

Wang

Dong

et al. 2022

IJMS

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Reproductive-stage heat stress (RSHS) poses a major constraint to cereal crop production by damaging main plant reproductive structures and hampering reproductive processes, including pollen and stigma viability, pollination, fertilization, grain setting and grain filling. Despite this well-recognized fact, research on crop heat stress (HS) is relatively recent compared to other abiotic stresses, such as drought and salinity, and in particular, RSHS studies in cereals are considerably few in comparison with seedling-stage and vegetative-stage-centered studies. Meanwhile, climate change-exacerbated HS, independently or synergistically with drought, will have huge implications on crop performance and future global food security. Fortunately, due to their sedentary nature, crop plants have evolved complex and diverse transient and long-term mechanisms to perceive, transduce, respond and adapt to HS at the molecular, cell, physiological and whole plant levels. Therefore, uncovering the molecular and physiological mechanisms governing plant response and tolerance to RSHS facilitates the designing of effective strategies to improve HS tolerance in cereal crops. In this review, we update our understanding of several aspects of RSHS in cereals, particularly impacts on physiological processes and yield; HS signal perception and transduction; and transcriptional regulation by heat shock factors and heat stress-responsive genes. We also discuss the epigenetic, post-translational modification and HS memory mechanisms modulating plant HS tolerance. Moreover, we offer a critical set of strategies (encompassing genomics and plant breeding, transgenesis, omics and agronomy) that could accelerate the development of RSHS-resilient cereal crop cultivars. We underline that a judicious combination of all of these strategies offers the best foot forward in RSHS tolerance improvement in cereals. Further, we highlight critical shortcomings to RSHS tolerance investigations in cereals and propositions for their circumvention, as well as some knowledge gaps, which should guide future research priorities. Overall, our review furthers our understanding of HS tolerance in plants and supports the rational designing of RSHS-tolerant cereal crop cultivars for the warming climate.

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Section: Genomic Selection and Modern Plant-breeding Methodsmentioning

confidence: 99%

Reproductive-Stage Heat Stress in Cereals: Impact, Plant Responses and Strategies for Tolerance Improvement

Zenda

Wang

Dong

et al. 2022

IJMS

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“…Furthermore, effective crop breeding programs with an improved genetic base will speed up fast-forward breeding, proposed by Varshney et al (2021b) . Briefly, genomics-assisted breeding, including haplotype-GWAS, haplotype-assisted breeding, and haplotype-assisted genomic selection, will effectively utilize superior haplotypes to accelerate future breeding advancement ( Bhat et al, 2021 ). Moreover, modern machine learning tools and artificial intelligence methodologies systematically incorporate the overflow of data rolling through multi-omics approaches ( van Dijk et al, 2020 ; Jung et al, 2021 ).…”

Section: Conclusion and Future Prospectsmentioning

confidence: 99%

Advances in “Omics” Approaches for Improving Toxic Metals/Metalloids Tolerance in Plants

et al. 2022

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Food safety has emerged as a high-urgency matter for sustainable agricultural production. Toxic metal contamination of soil and water significantly affects agricultural productivity, which is further aggravated by extreme anthropogenic activities and modern agricultural practices, leaving food safety and human health at risk. In addition to reducing crop production, increased metals/metalloids toxicity also disturbs plants’ demand and supply equilibrium. Counterbalancing toxic metals/metalloids toxicity demands a better understanding of the complex mechanisms at physiological, biochemical, molecular, cellular, and plant level that may result in increased crop productivity. Consequently, plants have established different internal defense mechanisms to cope with the adverse effects of toxic metals/metalloids. Nevertheless, these internal defense mechanisms are not adequate to overwhelm the metals/metalloids toxicity. Plants produce several secondary messengers to trigger cell signaling, activating the numerous transcriptional responses correlated with plant defense. Therefore, the recent advances in omics approaches such as genomics, transcriptomics, proteomics, metabolomics, ionomics, miRNAomics, and phenomics have enabled the characterization of molecular regulators associated with toxic metal tolerance, which can be deployed for developing toxic metal tolerant plants. This review highlights various response strategies adopted by plants to tolerate toxic metals/metalloids toxicity, including physiological, biochemical, and molecular responses. A seven-(omics)-based design is summarized with scientific clues to reveal the stress-responsive genes, proteins, metabolites, miRNAs, trace elements, stress-inducible phenotypes, and metabolic pathways that could potentially help plants to cope up with metals/metalloids toxicity in the face of fluctuating environmental conditions. Finally, some bottlenecks and future directions have also been highlighted, which could enable sustainable agricultural production.

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“…The haplotype is a collection of specific alleles in a cluster of tightly linked genes that are likely to be inherited together; hence, they are likely to be conserved as a sequence [47]. The genes bZIP, Ann1, chlorophyll a-b binding protein, and AtBG1 identified across the millet species showed highly conserved regions with a high number of haplotypes.…”

Section: Drought Gene Haplotype Identification In Millet Cropsmentioning

confidence: 99%

Identification of Candidate Genes Regulating Drought Tolerance in Pearl Millet

Chakraborty

Viswanath

Malipatil

et al. 2022

IJMS

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Pearl millet is an important crop of the arid and semi-arid ecologies to sustain food and fodder production. The greater tolerance to drought stress attracts us to examine its cellular and molecular mechanisms via functional genomics approaches to augment the grain yield. Here, we studied the drought response of 48 inbreds representing four different maturity groups at the flowering stage. A set of 74 drought-responsive genes were separated into five major phylogenic groups belonging to eight functional groups, namely ABA signaling, hormone signaling, ion and osmotic homeostasis, TF-mediated regulation, molecular adaptation, signal transduction, physiological adaptation, detoxification, which were comprehensively studied. Among the conserved motifs of the drought-responsive genes, the protein kinases and MYB domain proteins were the most conserved ones. Comparative in-silico analysis of the drought genes across millet crops showed foxtail millet had most orthologs with pearl millet. Of 698 haplotypes identified across millet crops, MyC2 and Myb4 had maximum haplotypes. The protein–protein interaction network identified ABI2, P5CS, CDPK, DREB, MYB, and CYP707A3 as major hub genes. The expression assay showed the presence of common as well as unique drought-responsive genes across maturity groups. Drought tolerant genotypes in respective maturity groups were identified from the expression pattern of genes. Among several gene families, ABA signaling, TFs, and signaling proteins were the prospective contributors to drought tolerance across maturity groups. The functionally validated genes could be used as promising candidates in backcross breeding, genomic selection, and gene-editing schemes in pearl millet and other millet crops to increase the yield in drought-prone arid and semi-arid ecologies.

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Features and applications of haplotypes in crop breeding

Cited by 93 publications

References 158 publications

Reproductive-Stage Heat Stress in Cereals: Impact, Plant Responses and Strategies for Tolerance Improvement

Reproductive-Stage Heat Stress in Cereals: Impact, Plant Responses and Strategies for Tolerance Improvement

Advances in “Omics” Approaches for Improving Toxic Metals/Metalloids Tolerance in Plants

Identification of Candidate Genes Regulating Drought Tolerance in Pearl Millet

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