Translational genomics and molecular breeding for enhancing precision and efficiency in crop improvement programs: Some examples in legumes

Legumes like chickpea, pigeonpea and groundnut are protein rich, nutrient-dense, and nitrogen fixing crops. Their importance is increasingly recognized in view of the urgent need to address burgeoning malnutrition problem and to impart sustainability to cropping systems. Breeding programs in these crops have achieved great success. However, consistent improvement in genetic gains demands integration of innovative tools and technologies with crop breeding programs. Genomic resources are of paramount significance in context of improving the efficiency and precision of crop breeding schemes. The last decade has witnessed a remarkable success in generating unprecedented genomic resources in these crops, thus transforming these genomic orphans into genomic resource rich crops. These genomic resources include array-based genotyping platforms, high-resolution genetic linkage maps/HapMaps, comprehensive transcriptome assemblies and gene expression atlas, and whole genome sequences etc. Further progression from the training phase (development) to breeding (deployment) phase is marked with the current availability of a variety of molecular breeding products in these legume crops. In the present review, we discuss how deployment of the modern genomic resources such as next-generation gene discovery techniques and “gold standard experimental designs” is furthering our knowledge about the genetic underpinnings of trait variation. Also, key success stories demonstrating the power of molecular breeding in these legume crops are highlighted. It is opined that the breeding populations constantly improved by sequence-based breeding approach will greatly help improving breeding traits and the genetic gains accruable from crop breeding programs.

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LIMITATIONS TO THE USE OF PHYSIOLOGICAL VARIABILITY IN PLANT BREEDING

Canadian Journal of Plant Science ◽

10.4141/cjps83-002 ◽

1983 ◽

Vol 63 (1) ◽

pp. 11-21 ◽

Cited By ~ 32

Author(s):

JOHN D. MAHON

Keyword(s):

Genetic Variability ◽

Crop Improvement ◽

Breeding Programs ◽

Genetic Studies ◽

Physiological Diversity ◽

Physiological Processes ◽

Physiological Variability ◽

Genetic Heritability ◽

Improvement Programs ◽

Physiological Characters

The possibility that breeding programs may be reaching a point of limited progress because of the lack of genetic diversity has often been raised. However, there is also an often-expressed feeling that considerable genetic variability may exist in fundamental physiological processes. In this review, an attempt is made to examine whether there is evidence of genetic variability in quantitative physiological characters, and if so, whether such variability is likely to be useful to crop improvement programs. The results, presented from the literature and the author’s laboratory, indicate that physiological characters demonstrate considerable genotypic variability in expression. Moreover, in cases where genotype performance has been studied over a range of environments or where crossing studies have been carried out, physiological characters often have relatively high heritabilities. This suggests that, at least from a genetic standpoint, improvements in the expression of physiological processes may be possible. On the other hand, the problems of environmental sensitivity and its resultant error variability, combined with cumbersome methodology and complex physiological interactions, make it difficult to relate individual physiological characters to agronomic benefits, and make large genetic studies difficult. The exploitation of physiological diversity remains a major challenge to plant scientists.Key words: Genetic heritability, physiology of yield

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Quantitative Epigenetics: A New Avenue for Crop Improvement

Epigenomes ◽

10.3390/epigenomes4040025 ◽

2020 ◽

Vol 4 (4) ◽

pp. 25 ◽

Cited By ~ 1

Author(s):

Vijay Gahlaut ◽

Gaurav Zinta ◽

Vandana Jaiswal ◽

Sanjay Kumar

Keyword(s):

Molecular Breeding ◽

Recombinant Inbred Lines ◽

Crop Improvement ◽

Genotyping By Sequencing ◽

Phenotypic Traits ◽

Epigenetic Variation ◽

Epigenome Editing ◽

Epigenetic Diversity ◽

Improvement Programs

Plant breeding conventionally depends on genetic variability available in a species to improve a particular trait in the crop. However, epigenetic diversity may provide an additional tier of variation. The recent advent of epigenome technologies has elucidated the role of epigenetic variation in shaping phenotype. Furthermore, the development of epigenetic recombinant inbred lines (epi-RILs) in model species such as Arabidopsis has enabled accurate genetic analysis of epigenetic variation. Subsequently, mapping of epigenetic quantitative trait loci (epiQTL) allowed association between epialleles and phenotypic traits. Likewise, epigenome-wide association study (EWAS) and epi-genotyping by sequencing (epi-GBS) have revolutionized the field of epigenetics research in plants. Thus, quantitative epigenetics provides ample opportunities to dissect the role of epigenetic variation in trait regulation, which can be eventually utilized in crop improvement programs. Moreover, locus-specific manipulation of DNA methylation by epigenome-editing tools such as clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) can potentially facilitate epigenetic based molecular breeding of important crop plants.

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Sustainable Sesame (Sesamum indicum L.) Production through Improved Technology: An Overview of Production, Challenges, and Opportunities in Myanmar

Sustainability ◽

10.3390/su12093515 ◽

2020 ◽

Vol 12 (9) ◽

pp. 3515 ◽

Cited By ~ 1

Author(s):

Daisy Myint ◽

Syed A. Gilani ◽

Makoto Kawase ◽

Kazuo N. Watanabe

Keyword(s):

Crop Production ◽

Smallholder Farmers ◽

Crop Improvement ◽

Integrated Approach ◽

Sesamum Indicum ◽

Genetic Maps ◽

Limiting Factors ◽

Market Demand ◽

Genomic Resources ◽

Improvement Programs

This paper aims to review the research achievements concerning sustainable sesame (Sesamum indicum L.) production and outlook on the production constraints and future perspectives for Myanmar sesame. Sesame is an economically and nutritionally important crop, and it is prized for oil. The global sesame market demand is rising with increasing health awareness. Meanwhile, there is high competition in the market among producing countries for an international trade. Smallholder farmers in developing countries cultivate sesame as a cash crop on marginal soils. The edible oilseed sectors currently face several challenges, including ones affecting sesame crops. For sustainable production of sesame, an integrated approach is needed to overcome these challenges and the critical limiting factors should be identified. In recent years, sesame genomic resources, including molecular markers, genetic maps, genome sequences, and online functional databases, are available for sesame genetic improvement programs. Since ancient times, sesame has been cultivated in Myanmar, but productivity is still lower than that of other sesame producing countries. Myanmar sesame production is limited by many factors, including production technology, research and development, etc. With integration of these genomic resources, crop production and protection techniques, postharvest practices, crop improvement programs, and capacity building will play a crucial role for improving sesame production in Myanmar.

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Speed breeding: a powerful tool to accelerate crop research and breeding

10.1101/161182 ◽

2017 ◽

Cited By ~ 4

Author(s):

Amy Watson ◽

Sreya Ghosh ◽

Matthew J. Williams ◽

William S. Cuddy ◽

James Simmonds ◽

...

Keyword(s):

Plant Traits ◽

Crop Improvement ◽

Adult Plant ◽

Crop Breeding ◽

Improvement Rate ◽

Global Food Security ◽

Generation Times ◽

Improvement Programs ◽

Supplemental Lighting ◽

Rapid Generation

The growing human population and a changing environment have raised significant concern for global food security, with the current improvement rate of several important crops inadequate to meet future demand [1]. This slow improvement rate is attributed partly to the long generation times of crop plants. Here we present a method called ‘speed breeding’, which greatly shortens generation time and accelerates breeding and research programs. Speed breeding can be used to achieve up to 6 generations per year for spring wheat (Triticum aestivum), durum wheat (T. durum), barley (Hordeum vulgare), chickpea (Cicer arietinum), and pea (Pisum sativum) and 4 generations for canola (Brassica napus), instead of 2-3 under normal glasshouse conditions. We demonstrate that speed breeding in fully-enclosed controlled-environment growth chambers can accelerate plant development for research purposes, including phenotyping of adult plant traits, mutant studies, and transformation. The use of supplemental lighting in a glasshouse environment allows rapid generation cycling through single seed descent and potential for adaptation to larger-scale crop improvement programs. Cost-saving through LED supplemental lighting is also outlined. We envisage great potential for integrating speed breeding with other modern crop breeding technologies, including high-throughput genotyping, genome editing, and genomic selection, accelerating the rate of crop improvement.

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Trends of genetic changes uncovered by Env- and Eigen-GWAS in wheat and barley

10.1101/2020.11.27.400333 ◽

2020 ◽

Author(s):

Rajiv Sharma ◽

James Cockram ◽

Keith A. Gardner ◽

Joanne Russell ◽

Luke Ramsay ◽

...

Keyword(s):

Plant Breeding ◽

Crop Improvement ◽

Genome Structure ◽

Genomic Relationship Matrix ◽

Past Century ◽

Relationship Matrix ◽

Crop Breeding ◽

Phenotypic Data ◽

Improvement Programs ◽

Genomic Regions

AbstractThe process of crop breeding over the last century has delivered new varieties with increased genetic gains, resulting in higher crop performance and yield. However in many cases, the underlying alleles and genomic regions that have underpinned this success remain unknown. This is due, in part, to the difficulty in generating sufficient phenotypic data on large numbers of historical varieties to allow such analyses to be undertaken. Here we demonstrate the ability to circumvent such bottlenecks by identifying genomic regions selected over 100 years of crop breeding using the age of a variety as a surrogate for yield. Using ‘environmental genome-wide association scans’ (EnvGWAS) on variety age in two of the world’s most important crops, wheat and barley, we found strong signals of selection across the genomes of our target crops. EnvGWAS identified 16 genomic regions in barley and 10 in wheat with contrasting patterns between spring and winter types of the two crops. To further examine changes in genome structure in wheat and barley over the past century, we used the same genotypic data to derive eigenvectors for deployment in EigenGWAS. This resulted in the detection of seven major chromosomal introgressions that contributed to adaptation in wheat. The deployment of both EigenGWAS and EnvGWAS based on variety age avoids costly phenotyping and will facilitate the identification of genomic tracts that have been under selection during plant breeding in underutilized historical cultivar collections. Our results not only demonstrate the potential of using historical cultivar collections coupled with genomic data to identify chromosomal regions that have been under selection but to also guide future plant breeding strategies to maximise the rate of genetic gain and adaptation in crop improvement programs.Significance Statement100 years of plant breeding have greatly improved crop adaptation, resilience, and productivity. Generating the trait data required for these studies is prohibitively expensive and can be impossible on large historical traits. This study reports using variety age and eigenvectors of the genomic relationship matrix as surrogate traits in GWAS to locate the genomic regions that have undergone selection during varietal development in wheat and barley. In several cases these were confirmed as associated with yield and other selected traits. The success and the simplicity of the approach means it can easily be extended to other crops with a recent recorded history of plant breeding and available genomic resources.

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Prediction of genetic gains through selection of sweet potato accessions

Horticultura Brasileira ◽

10.1590/s0102-0536202004008 ◽

2020 ◽

Vol 38 (4) ◽

pp. 387-393

Author(s):

Pablo F Vargas ◽

Maria Eduarda F Otoboni ◽

Beatriz G Lopes ◽

Bruno E Pavan

Keyword(s):

Genetic Variability ◽

Sweet Potato ◽

Block Design ◽

Root Production ◽

Crop Breeding ◽

Breeding Programs ◽

High Genetic Variability ◽

Genetic Gains ◽

Randomized Block Design ◽

Future Population

ABSTRACT Due to the high genetic variability found in sweet potato and a low number of cultivars available on the market, there are opportunities for necessary improvements in crop breeding programs. The selection indexes are a favorable strategy to achieve higher yields through genetic gains obtained with the future population. Thus, the objective was to evaluate the selection gain of agronomic characters from sweet potato accessions for root production and dual-aptitude. 95 accessions and two commercial cultivars (Braslandia Branca and Brazlândia Roxa) were evaluated. A randomized block design with three replications of ten plants per plot was used. The index proposed by Mulamba & Mock was used to select superior individuals. The evaluated population showed high genetic variability providing considerable selection gains, being recommended some clones for tests of value for cultivation and use. The VR13-61 accession was the most recommended for root production and VR13-11 and VR13-22 for dual-aptitude.

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Estimation of soybean genetic progress in the South of Brazil using multi-environmental yield trials

Scientia Agricola ◽

10.1590/s0103-90162009000300005 ◽

2009 ◽

Vol 66 (3) ◽

pp. 309-316 ◽

Cited By ~ 10

Author(s):

Cláudia Erna Lange ◽

Luiz Carlos Federizzi

Keyword(s):

Cropping Systems ◽

Breeding Program ◽

Maturity Group ◽

Genetic Progress ◽

Data Set ◽

Early Maturity ◽

Breeding Programs ◽

Genetic Breeding ◽

Genetic Gains ◽

Maturity Groups

The success of a genetic breeding program in a certain period can be assessed by the genetic gain observed. Genetic progress can be estimated from the multi environmental trials (MET) data which are routinely carried out by annual species breeding programs for the assessment of new commercial cultivars. A data set of 20 years of MET of advanced soybean lines derived from four breeding programs was used to estimate and to compare the genetic gains obtained for three soybean maturity groups (early, medium and late) in four cropping regions of the State of Rio Grande do Sul. The estimated yield gains ranged from 0.0 to 71.5 kg ha-1 year-1 (3.49% per year), depending on the maturity group and region, which suggests that the genetic breeding effort does not have a similar effect among the maturity groups or benefit the regions equally. There was no evidence of genetic progress for the early maturity group in any of the four regions, whereas gains in Regions I and IV were comparatively greater than those in Regions II and III. The objectives of the soybean breeding program in the region should be redirected. Since not all the experimental lines used to estimate genetic gains were commercially released, the reported genetics gains were achieved by the breeding programs rather than those achieved by the cropping systems.

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Fab Advances in Fabaceae for Abiotic Stress Resilience: From ‘Omics’ to Artificial Intelligence

International Journal of Molecular Sciences ◽

10.3390/ijms221910535 ◽

2021 ◽

Vol 22 (19) ◽

pp. 10535

Author(s):

Dharmendra Singh ◽

Priya Chaudhary ◽

Jyoti Taunk ◽

Chandan Kumar Singh ◽

Deepti Singh ◽

...

Keyword(s):

Artificial Intelligence ◽

Abiotic Stress ◽

Stress Response ◽

Abiotic Stress Tolerance ◽

Crop Improvement ◽

Genetic Determinants ◽

Diverse Range ◽

Food Legume ◽

Legume Crops ◽

Improvement Programs

Legumes are a better source of proteins and are richer in diverse micronutrients over the nutritional profile of widely consumed cereals. However, when exposed to a diverse range of abiotic stresses, their overall productivity and quality are hugely impacted. Our limited understanding of genetic determinants and novel variants associated with the abiotic stress response in food legume crops restricts its amelioration. Therefore, it is imperative to understand different molecular approaches in food legume crops that can be utilized in crop improvement programs to minimize the economic loss. ‘Omics’-based molecular breeding provides better opportunities over conventional breeding for diversifying the natural germplasm together with improving yield and quality parameters. Due to molecular advancements, the technique is now equipped with novel ‘omics’ approaches such as ionomics, epigenomics, fluxomics, RNomics, glycomics, glycoproteomics, phosphoproteomics, lipidomics, regulomics, and secretomics. Pan-omics—which utilizes the molecular bases of the stress response to identify genes (genomics), mRNAs (transcriptomics), proteins (proteomics), and biomolecules (metabolomics) associated with stress regulation—has been widely used for abiotic stress amelioration in food legume crops. Integration of pan-omics with novel omics approaches will fast-track legume breeding programs. Moreover, artificial intelligence (AI)-based algorithms can be utilized for simulating crop yield under changing environments, which can help in predicting the genetic gain beforehand. Application of machine learning (ML) in quantitative trait loci (QTL) mining will further help in determining the genetic determinants of abiotic stress tolerance in pulses.

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Quantitative Epigenetics: A New Avenue for Crop Improvement

10.20944/preprints202009.0348.v1 ◽

2020 ◽

Author(s):

Vijay Gahlaut ◽

Gaurav Zinta ◽

Vandana Jaiswal

Keyword(s):

Molecular Breeding ◽

Recombinant Inbred Lines ◽

Crop Improvement ◽

Phenotypic Traits ◽

Epigenetic Variation ◽

Model Species ◽

Epigenome Editing ◽

Epigenetic Diversity ◽

Improvement Programs

Plant breeding conventionally depends on genetic variability available in a species to improve a particular trait in the crop. However, epigenetic diversity may provide an additional tier of variation. The recent advent of epigenome technologies has elucidated the role of epigenetic variation in shaping phenotype. Further, the development of epigenetic recombinant inbred lines (epi-RILs) in the model species such as Arabidopsis has enabled accurate genetic analysis of epigenetic variation. Subsequently, mapping of epigenetic quantitative trait loci (epiQTL) allowed association between epialleles and phenotypic traits. Thus, quantitative epigenetics provides ample opportunities to dissect the role of epigenetic variation in trait regulation, which can be eventually utilized in crop improvement programs. Moreover, locus-specific manipulation of DNA methylation by epigenome-editing tools such as clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) can facilitate epigenetic based molecular breeding of important crop plants.

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Quantitative Epigenetics: A New Avenue for Crop Improvement

10.20944/preprints202009.0348.v2 ◽

2020 ◽

Author(s):

Vijay Gahlaut ◽

Gaurav Zinta ◽

Vandana Jaiswal ◽

Sanjay Kumar

Keyword(s):

Molecular Breeding ◽

Recombinant Inbred Lines ◽

Crop Improvement ◽

Phenotypic Traits ◽

Epigenetic Variation ◽

Model Species ◽

Epigenome Editing ◽

Epigenetic Diversity ◽

Improvement Programs

Plant breeding conventionally depends on genetic variability available in a species to improve a particular trait in the crop. However, epigenetic diversity may provide an additional tier of variation. The recent advent of epigenome technologies has elucidated the role of epigenetic variation in shaping phenotype. Further, the development of epigenetic recombinant inbred lines (epi-RILs) in the model species such as Arabidopsis has enabled accurate genetic analysis of epigenetic variation. Subsequently, mapping of epigenetic quantitative trait loci (epiQTL) allowed association between epialleles and phenotypic traits. Thus, quantitative epigenetics provides ample opportunities to dissect the role of epigenetic variation in trait regulation, which can be eventually utilized in crop improvement programs. Moreover, locus-specific manipulation of DNA methylation by epigenome-editing tools such as clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) can facilitate epigenetic based molecular breeding of important crop plants.

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