Advanced analytics, phenomics and biotechnology approaches to enhance genetic gains in plant breeding

Dwivedi, Sangam L.; Goldman, Irwin L.; Ceccarelli, Salvatore; Ortíz, Rodomiro

doi:10.1016/bs.agron.2020.02.002

Cited by 24 publications

(17 citation statements)

References 198 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Based on the results, it known that geographic location does not affect the grouping of this germplasm. According to Dwivedi et al (2020), geographic location is unusually related to the emerge of genetic diversity. It means that genotypes originating from the same region are not always in the same cluster.…”

Section: Discussionmentioning

confidence: 99%

Genetic evaluation of tidal swamp rice from South Kalimantan, Indonesia based on the agro-morphological markers

Mursyidin

Khairullah

2020

Biodiversitas

View full text Add to dashboard Cite

Abstract. Mursyidin DH, Khairullah I. 2020. Genetic evaluation of tidal swamp rice from South Kalimantan, Indonesia based on the agro-morphological markers. Biodiversitas 21: 4795-4803. A total of 71 cultivars of the tidal swamp rice (Oryza sativa L.), originated mainly from South Kalimantan, Indonesia, were evaluated agro-morphologically by using 26 qualitative and 13 quantitative traits. Based on these traits, this germplasm is generally low in diversity. However, three agro-morphological traits, namely the tillering abilities, seedling height, and diameter of the basal internode, shows the relatively highest diversity, shown by the Lakatan Putih, Pandak Putih, and Bayar Papuyu, respectively. The UPGMA and PCA revealed that this germplasm divided into six main clusters, where the sixth cluster is the largest with a total membership of 60 cultivars. The cluster analysis also revealed that Lakatan Siam is far separate from other cultivars. Thus, this finding might be useful in the future rice breeding programs, particularly in developing new rice cultivar for the tidal swamp areas.

show abstract

Section: Discussionmentioning

confidence: 99%

Genetic evaluation of tidal swamp rice from South Kalimantan, Indonesia based on the agro-morphological markers

Mursyidin

Khairullah

2020

Biodiversitas

View full text Add to dashboard Cite

show abstract

“…3) revealed that geographical locations did not affect the germplasm grouping. According to Dwivedi et al (2020), this parameter is not usually related to emerging genetic diversity, indicating that genotypes originating from the same region will not always be grouped within the same cluster. However, PCA showed a unique feature, where some of the germplasm was grouped by their agro-morphological characters.…”

Section: Genetic Relationship and Its Implicationsmentioning

confidence: 99%

Genetic diversity and relationship of Indonesian swamp rice (Oryza sativa L.) germplasm based on agro-morphological markers

2022

ANRES

View full text Add to dashboard Cite

Importance of the work: Swamp rice (Oryza sativa L.) is essential germplasm for future rice breeding because of some agronomical characters or functional genes. Objectives: The genetic diversity and relationship was determined of 108 cultivars of Indonesian swamp rice using 31 agro-morphological markers to identify the distinctiveness of the characters that contributed to the genetic diversity based on Pearson correlation analysis among these characters. Materials & Methods:The standardized Shannon diversity index (H') was used to determine the genetic diversity of the germplasm. Principal components analysis (PCA) and the unweighted pair group method with arithmetic mean (UPGMA) were used to identify the distinctiveness of the characters that contributed to the genetic diversity and to reconstruct relationships. Results: This germplasm was generally low in genetic diversity (Shannon index value of 0.31 for qualitative and 0.36 for quantitative traits). However, two agro-morphological characters, namely the flag leaf attitude and culm diameter of the basal internode, had the highest diversity (H' = 0.68 and 0.97, respectively). PCA confirmed that these two characters contributed significantly to the emerging phenomenon. The culm diameter of the basal internode had a moderate correlation with panicle length and the panicle number of the primary and the secondary basal branches (r = 0.44-0.67). The UPGMA revealed that this germplasm was grouped into nine clusters, with the eighth being the largest (71 cultivars). In addition, the UPGMA revealed that some cultivars had closest relationships, such as Unyil with Karat Kaleng and Pelita Rampak versus Katimuri. Conversely, the farthest relationships were for Sawah Kanyut versus Siam Gumpal and Siam Salawi versus Siam Gumpal. Main finding: This information might be useful in future rice breeding programs, particularly in developing new rice cultivars for swamp areas.

show abstract

“…In GS, genome-wide high throughput markers (such as SNPs) that are in LD with QTLs are used to estimate their effects through optimum statistical models, before genomic estimated breeding values (GEBVs) are computed for each individual to select potential elite lines ( Shamshad and Sharma, 2018 ; Mérida-García et al, 2019 ; Voss-Fels et al, 2019 ). Two population types are a pre-requisite in GS, viz., a training/reference population comprised of a cohort of individuals with both genotypic and phenotypic data and a testing/breeding population consisting of candidate breeding lines with genotypic data only ( Dwivedi et al, 2020 ; Xu et al, 2020 ). The predicted GEBVs are then used for selection, excluding the need for further phenotyping ( Srivastava et al, 2020 ; Zenda et al, 2021 ).…”

Section: Genomics and Pan-genomicsmentioning

confidence: 99%

Omics-Facilitated Crop Improvement for Climate Resilience and Superior Nutritive Value

et al. 2021

View full text Add to dashboard Cite

Novel crop improvement approaches, including those that facilitate for the exploitation of crop wild relatives and underutilized species harboring the much-needed natural allelic variation are indispensable if we are to develop climate-smart crops with enhanced abiotic and biotic stress tolerance, higher nutritive value, and superior traits of agronomic importance. Top among these approaches are the “omics” technologies, including genomics, transcriptomics, proteomics, metabolomics, phenomics, and their integration, whose deployment has been vital in revealing several key genes, proteins and metabolic pathways underlying numerous traits of agronomic importance, and aiding marker-assisted breeding in major crop species. Here, citing several relevant examples, we appraise our understanding on the recent developments in omics technologies and how they are driving our quest to breed climate resilient crops. Large-scale genome resequencing, pan-genomes and genome-wide association studies are aiding the identification and analysis of species-level genome variations, whilst RNA-sequencing driven transcriptomics has provided unprecedented opportunities for conducting crop abiotic and biotic stress response studies. Meanwhile, single cell transcriptomics is slowly becoming an indispensable tool for decoding cell-specific stress responses, although several technical and experimental design challenges still need to be resolved. Additionally, the refinement of the conventional techniques and advent of modern, high-resolution proteomics technologies necessitated a gradual shift from the general descriptive studies of plant protein abundances to large scale analysis of protein-metabolite interactions. Especially, metabolomics is currently receiving special attention, owing to the role metabolites play as metabolic intermediates and close links to the phenotypic expression. Further, high throughput phenomics applications are driving the targeting of new research domains such as root system architecture analysis, and exploration of plant root-associated microbes for improved crop health and climate resilience. Overall, coupling these multi-omics technologies to modern plant breeding and genetic engineering methods ensures an all-encompassing approach to developing nutritionally-rich and climate-smart crops whose productivity can sustainably and sufficiently meet the current and future food, nutrition and energy demands.

show abstract

Advanced analytics, phenomics and biotechnology approaches to enhance genetic gains in plant breeding

Cited by 24 publications

References 198 publications

Genetic evaluation of tidal swamp rice from South Kalimantan, Indonesia based on the agro-morphological markers

Genetic evaluation of tidal swamp rice from South Kalimantan, Indonesia based on the agro-morphological markers

Genetic diversity and relationship of Indonesian swamp rice (Oryza sativa L.) germplasm based on agro-morphological markers

Omics-Facilitated Crop Improvement for Climate Resilience and Superior Nutritive Value

Contact Info

Product

Resources

About