scholarly journals Genomics and breeding innovations for enhancing genetic gain for climate resilience and nutrition traits

2021 ◽  
Author(s):  
Pallavi Sinha ◽  
Vikas K. Singh ◽  
Abhishek Bohra ◽  
Arvind Kumar ◽  
Jochen C. Reif ◽  
...  
Keyword(s):  
Statistical Methods ◽  
Genetic Gain ◽  
Crop Improvement ◽  
Breeding Population ◽  
Breeding Cycle ◽  
Climate Resilience ◽  
Heritability Estimation ◽  
Improvement Programs ◽  
Statistical Designs ◽  
Novel Alleles

Abstract Key message Integrating genomics technologies and breeding methods to tweak core parameters of the breeder’s equation could accelerate delivery of climate-resilient and nutrient rich crops for future food security. Abstract Accelerating genetic gain in crop improvement programs with respect to climate resilience and nutrition traits, and the realization of the improved gain in farmers’ fields require integration of several approaches. This article focuses on innovative approaches to address core components of the breeder’s equation. A prerequisite to enhancing genetic variance (σ2g) is the identification or creation of favorable alleles/haplotypes and their deployment for improving key traits. Novel alleles for new and existing target traits need to be accessed and added to the breeding population while maintaining genetic diversity. Selection intensity (i) in the breeding program can be improved by testing a larger population size, enabled by the statistical designs with minimal replications and high-throughput phenotyping. Selection priorities and criteria to select appropriate portion of the population too assume an important role. The most important component of breeder′s equation is heritability (h2). Heritability estimates depend on several factors including the size and the type of population and the statistical methods. The present article starts with a brief discussion on the potential ways to enhance σ2g in the population. We highlight statistical methods and experimental designs that could improve trait heritability estimation. We also offer a perspective on reducing the breeding cycle time (t), which could be achieved through the selection of appropriate parents, optimizing the breeding scheme, rapid fixation of target alleles, and combining speed breeding with breeding programs to optimize trials for release. Finally, we summarize knowledge from multiple disciplines for enhancing genetic gains for climate resilience and nutritional traits.

scholarly journals Current Advancements and Limitations of Gene Editing in Orphan Crops

2021 ◽  
Vol 12 ◽  
Author(s):  
Matthew Venezia ◽  
Kate M. Creasey Krainer
Keyword(s):  
Gene Editing ◽  
Crop Improvement ◽  
Screening Methods ◽  
In Planta ◽  
Base Editing ◽  
Guide Rna ◽  
Orphan Crops ◽  
Associated Proteins ◽  
Improvement Programs ◽  
Novel Alleles

Gene editing provides precise, heritable genome mutagenesis without permanent transgenesis, and has been widely demonstrated and applied in planta. In the past decade, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated proteins (Cas) has revolutionized the application of gene editing in crops, with mechanistic advances expanding its potential, including prime editing and base editing. To date, CRISPR/Cas has been utilized in over a dozen orphan crops with diverse genetic backgrounds, leading to novel alleles and beneficial phenotypes for breeders, growers, and consumers. In conjunction with the adoption of science-based regulatory practices, there is potential for CRISPR/Cas-mediated gene editing in orphan crop improvement programs to solve a plethora of agricultural problems, especially impacting developing countries. Genome sequencing has progressed, becoming more affordable and applicable to orphan crops. Open-access resources allow for target gene identification and guide RNA (gRNA) design and evaluation, with modular cloning systems and enzyme screening methods providing experimental feasibility. While the genomic and mechanistic limitations are being overcome, crop transformation and regeneration continue to be the bottleneck for gene editing applications. International collaboration between all stakeholders involved in crop improvement is vital to provide equitable access and bridge the scientific gap between the world’s most economically important crops and the most under-researched crops. This review describes the mechanisms and workflow of CRISPR/Cas in planta and addresses the challenges, current applications, and future prospects in orphan crops.

Effect of controlling future rate of inbreeding on expected genetic gain and genetic variability in small livestock populations

2020 ◽  
Vol 60 (14) ◽  
pp. 1681
Author(s):  
S. I. Mwangi ◽  
T. K. Muasya ◽  
E. D. Ilatsia ◽  
A. K. Kahi
Keyword(s):  
Genetic Variability ◽  
Milk Yield ◽  
Genetic Gain ◽  
Genetic Relationships ◽  
Breeding Population ◽  
Breeding Values ◽  
Sahiwal Cows ◽  
Improvement Programs ◽  
Small Livestock ◽  
Estimated Breeding Values

Context In the present study we assessed the use of average relationship as a means to control future rates of inbreeding in small cattle closed nucleus and its effect on genetic gain for milk yield as a means of managing genetic variability in livestock improvement programs. Aim The aim was to strike an ideal balance between genetic gain and loss of genetic variability for Sahiwal population. Methods A total of 8452 milk yield records of Sahiwal cows from National Sahiwal Stud, Kenya, were used to estimate breeding values and 19315 records used to estimate average relatedness of all individuals. The estimated breeding values and genetic relationships were then used to optimise individual genetic contributions between the best two males and the top 210 females in 2000–2008-year group, as well as between the best four, six and eight males and top, 420, 630 and 840 females based on estimated breeding values for lactation milk yield. Weights on genetic merit and average relationship considered in this study were (1, 0), (1, −300), (1, −500), (1, −1000) and (0, −1). Key results When the best sires were selected and used for mating disregarding average relationship with their mates i.e. (0, –1), genetic gain of up to 213 kg was realised accompanied by a rate of inbreeding per generation of 4%. Restricting average relationship alone i.e. (0, –1), resulted in a future rate of inbreeding of 1.6% and average merit of 154 when top two sires were used for breeding. At the same restriction level but using eight top sires, the rate of inbreeding per generation was 0.9% accompanied by an average merit of 128.2 kg. Controlling average relationship between mates resulted in increased genetic variability i.e. lower rate of inbreeding though average merit declined. Conclusion A rate of inbreeding per generation of <1% is required for a population to maintain its long-term viability. For this level to be attained, the size of the breeding population should be increased from the current two sires vs 210 dams to eight sires vs 840 dams. Implications Practical implications for closed nucleus programs such as the Sahiwal program in Kenya should include expanding the nucleus to comprise other institutional and privately-owned herds.

scholarly journals Plant genetic resources management and pre-breeding in genomics era

2019 ◽  
Vol 79 (01S) ◽  
Author(s):  
Kuldeep Singh ◽  
Sandeep Kumar ◽  
S. Raj Kumar ◽  
Mohar Singh ◽  
Kavita Gupta
Keyword(s):  
Genetic Variability ◽  
Genetic Resources ◽  
Complex Traits ◽  
Plant Genetic Resources ◽  
Crop Improvement ◽  
Breeding Cycle ◽  
Promising Alternative ◽  
Genetic Resources Management ◽  
Genomic Tools ◽  
Improvement Programs

Plant Genetic Resources (PGR) conserved in gene bank provides genetic variability for efficient utilization in breeding programmes. Pre-breeding is required for broadening the genetic base of the crop through identification of useful traits in un-adapted materials and transfer them into better adapted ones for further breeding. So, pre-breeding is a promising alternative (due to use of un-adapted materials) to link genetic resources and breeding programs. Utilization of PGR in crop improvement programmes including prebreeding have been very limited. Advances in genomics have provided us with high-quality reference genomes, sequencing and re-sequencing platforms with reduced cost, marker and QTL assisted selection, genomic selection and population level genotyping platforms. Further, genome editing tools like, CRISPR/Cas9 and its latest modification base editing technology can be used to generate target specific mutants and are important for establishing gene functions with respect to their phenotypes through developing knockout mutations. These new genomic tools can be used to generate, analyse and manipulate the genetic variability for designing cultivars with the desired traits. The genomic tools has not only accelerated the utilization of PGR but also assisted pre-breeding through rapid selection of trait-specific germplasm, reduced periods in breeding cycle for confirming gene of interest in intermediate material and validation of transfer of gene of interest in the cultivated gene pool. In crops, where limited genetic and genomic resources are available, pre-breeding becomes very challenging. We can say that genomics assisted utilization of PGR and prebreeding has accelerated the pace of introgression of complex traits in different crop cultivars.and yield plateau has already been achieved in these cultivars (Chen et al. 2014a). Under these circumstances, use of Plant Genetic Resources (PGR) in crop improvement programs provides an avenue to solve the problem.

scholarly journals Increasing selection gain and accuracy of harvest prediction models in Jatropha through genome-wide selection

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Adriano dos Santos ◽  
Erina Vitório Rodrigues ◽  
Bruno Galvêas Laviola ◽  
Larissa Pereira Ribeiro Teodoro ◽  
Paulo Eduardo Teodoro ◽  
...  
Keyword(s):  
Prediction Models ◽  
Block Design ◽  
Phenotypic Selection ◽  
Breeding Population ◽  
Breeding Cycle ◽  
Selection Cycle ◽  
Genome Wide ◽  
Random Block ◽  
Random Block Design ◽  
Number Of Individuals

AbstractGenome-wide selection (GWS) has been becoming an essential tool in the genetic breeding of long-life species, as it increases the gain per time unit. This study had a hypothesis that GWS is a tool that can decrease the breeding cycle in Jatropha. Our objective was to compare GWS with phenotypic selection in terms of accuracy and efficiency over three harvests. Models were developed throughout the harvests to evaluate their applicability in predicting genetic values in later harvests. For this purpose, 386 individuals of the breeding population obtained from crossings between 42 parents were evaluated. The population was evaluated in random block design, with six replicates over three harvests. The genetic effects of markers were predicted in the population using 811 SNP's markers with call rate = 95% and minor allele frequency (MAF) > 4%. GWS enables gains of 108 to 346% over the phenotypic selection, with a 50% reduction in the selection cycle. This technique has potential for the Jatropha breeding since it allows the accurate obtaining of GEBV and higher efficiency compared to the phenotypic selection by reducing the time necessary to complete the selection cycle. In order to apply GWS in the first harvests, a large number of individuals in the breeding population are needed. In the case of few individuals in the population, it is recommended to perform a larger number of harvests.

Proteomics Variation in Nigella Sativa L. (Rananculaceae) Germplasm

2021 ◽  
Vol 50 (2) ◽  
pp. 289-294
Author(s):  
Muhammad Sajjad Iqbal ◽  
Abdul Ghafoor
Keyword(s):  
Euclidean Distance ◽  
Nigella Sativa ◽  
Crop Improvement ◽  
Band Formation ◽  
First Report ◽  
Sds Page ◽  
Genetic Pattern ◽  
Specific Variation ◽  
Improvement Programs ◽  
Single Seeds

Study revealed a first report of proteomics variation in Nigella sativa L. based on analyzing 32 accessions through SDS-PAGE. Three prominent regions along eight subunits were identified. Intra specific variation was observed low whereas the sharpness of bands was high between first and second regions. It was noted that in second region there was no clear evidence of band formation in N. sativa. Prominent and sharp protein peptide bands were recorded in four accessions, namely PK-020561, PK-020609, PK-020620 and PK-020646. Further investigation of single seeds showed almost similar genetic pattern within the single accession. Five clusters were formed on the basis of Euclidean distance. Cluster-I & II contain 1, 1 accession each, likewise Cluster-III and C-IV contain 2, 2 accessions whereas Cluster-V was found diversified as consisted of 26 accessions. Two accessions PK-020878 and PK-020877 were recommended for polymorphism and crop improvement programs. Bangladesh J. Bot. 50(2): 289-294, 2021 (June)

Multivariate analyses of indigenous bread wheat (Triticum aestivum L.) landraces of Oman

2021 ◽  
pp. 483
Author(s):  
Ali Hussain Al Lawati ◽  
Saleem Kaseemsaheb Nadaf ◽  
Nadiya Abubakar Al Saady ◽  
Saleh Ali Al Hinai ◽  
Almandhar Almamari ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Bread Wheat ◽  
Multivariate Analyses ◽  
Crop Improvement ◽  
Winter Season ◽  
Principal Component ◽  
Triticum Aestivum L ◽  
Plant Parts ◽  
Improvement Programs ◽  
D Values

Oman is endowed with enormous diversity of important food crops that have global significance for food security and has ancient history of cultivation of bread wheat (Triticum aestivum L.) with its divergent landraces, which are useful in crop improvement. 55 indigenous Omani accessions conserved at the USDA were evaluated in the winter season (November to April) of the years 2017-2018 and 2018-2019 on loamy soil under sprinklers in augmented design with 5 check varieties in 5 replications following crop husbandry practices as per national recommendations using 9 quantitative (descriptors) and 6 qualitative traits (anthocyanin pigmentation on plant parts). The data on traits were subjected not only for PC values and D values after varimax rotation through Kaiser normalization in Principal Component Analysis (PCA) but also for Agglomerative Hierarchical Clustering (AHC). The results indicated that indigenous bread wheat accessions were significantly different (p>0.05) for all the quantitative traits except number of tillers. The multivariate analyses led to formation of four diverse clusters from PCA analyses corresponding to four quadrants of bi-plot graphs and three clusters from AHC analysis corresponding to main clades of dendrogram. The parents were selected from common accessions of distinct clusters in all the multivariate analyses for hybridization for improving characters of growth for higher yield or productivity with pigmentation on one or two plant parts useful for DUS test of varieties. The indigenous bread wheat landraces / accessions were genetically diverse and have potential for use in national crop improvement programs for earliness and higher grain productivity with distinct identification markers.

scholarly journals Population structure and genetic diversity analysis in Sali (Oryza sativa) rice germplasm of Assam using microsatellite markers

2021 ◽  
Vol 58 (2) ◽  
pp. 279-286
Author(s):  
Sandhani Saikia ◽  
Pratap Jyoti Handique ◽  
Mahendra K Modi
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Genetic Improvement ◽  
Crop Improvement ◽  
Mean Value ◽  
Diversity Analysis ◽  
Rice Cultivars ◽  
Improvement Program ◽  
Information Index ◽  
Improvement Programs

Genetic diversity is the source of novel allelic combinations that can be efficiently utilized in any crop improvement program. To facilitate future crop improvement programs in rice, a study was designed to identify the underlying genetic variations in the Sali rice germplasms of Assam using SSR markers. The 129 SSR markers that were used in the study amplified a total of 765 fragments with an average of 5.93 alleles per locus. The Shannon's Information Index was found to be in the range from 0.533 to 1.786. The Polymorphism Information Content (PIC) fell into the range from 0.304 to 0.691 with a mean value of 0.55. The overall FST value was found to be 0.519 that indicated the presence of genetic differentiation amongst the genotypes used in the study. The Sali population was divided into two clusters. The information obtained from the present study will facilitate the genetic improvement of Sali rice cultivars.

scholarly journals Sorghum pan-genome explores the functional utility to accelerate the genetic gain

2021 ◽  
Author(s):  
Pradeep Ruperao ◽  
Nepolean Thirunavukkarasu ◽  
Prasad Gandham ◽  
Sivasubramani S. ◽  
Govindaraj M ◽  
...  
Keyword(s):  
Genetic Gain ◽  
Core Genome ◽  
Agronomic Traits ◽  
Crop Improvement ◽  
Genomic Diversity ◽  
Pan Genome ◽  
Genome Association ◽  
Reference Genomes ◽  
Insight Into ◽  
Variable Genes

AbstractSorghum (Sorghum bicolor L.) is one of the most important food crops in the arid and rainfed production ecologies. It is a part of resilient farming and is projected as a smart crop to overcome the food and nutritional challenges in the developing world. The development and characterisation of the sorghum pan-genome will provide insight into genome diversity and functionality, supporting sorghum improvement. We built a sorghum pan-genome using reference genomes as well as 354 genetically diverse sorghum accessions belonging to different races. We explored the structural and functional characteristics of the pan-genome and explain its utility in supporting genetic gain. The newly-developed pan-genome has a total of 35,719 genes, a core genome of 16,821 genes and an average of 32,795 genes in each cultivar. The variable genes are enriched with environment responsive genes and classify the sorghum accessions according to their race. We show that 53% of genes display presence-absence variation, and some of these variable genes are predicted to be functionally associated with drought traits. Using more than two million SNPs from the pan-genome, association analysis identified 398 SNPs significantly associated with important agronomic traits, of which, 92 were in genes. Drought gene expression analysis identified 1,788 genes that are functionally linked to different conditions, of which 79 were absent from the reference genome assembly. This study provides comprehensive genomic diversity resources in sorghum which can be used in genome assisted crop improvement.

New and novel genetic tools for improving crops.

2021 ◽  
Vol 16 (028) ◽  
Author(s):  
Penna Suprasanna
Keyword(s):  
Plant Breeding ◽  
Agronomic Traits ◽  
Plant Traits ◽  
Crop Improvement ◽  
Genetically Modified Crops ◽  
Climate Resilience ◽  
Crop Varieties ◽  
New Novel ◽  
High Throughput Phenotyping ◽  
Sequencing Platforms

Abstract The basic tenet of crop improvement is the novel genetic variability that is achieved through selection, hybridization, mutation and recombination. The new technological innovations of plant breeding offer scope for transforming crop improvement with more precision and resolution. Advances in genomic-based tools and high-throughput phenotyping have enabled the analysis of genetic variation and identification of molecular signatures of agronomic traits. Molecular markers and molecular-marker-assisted breeding have facilitated the speedy selection of new, novel genetic combinations in breeding for high-yielding, stress-tolerant and nutritionally enriched crops. Transgenic methods have revolutionized modification for stress tolerance and higher productivity, and several genetically modified crops are under cultivation. Availability of genome sequencing platforms and genomic resources has significantly contributed to accessing novel genes and validating their functions. Genome-editing tools and recent advances of prime editing are now accessible for precise genetic alteration of plant traits. The new plant breeding tools will certainly foster development of highly productive, improved crop varieties for achieving food security and climate resilience.

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