Genomics-Assisted Plant Breeding in the 21st Century: Technological Advances and Progress

Kumpatla, Siva P.; Buyyarapu, Ramesh; Abdurakhmonov, Ibrokhim Y.; Mammadov, Jafar

doi:10.5772/37458

Cited by 16 publications

(3 citation statements)

References 178 publications

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“…The biggest driving force for genomics-assisted crop breeding in the plant genomics era has been the inexpensive sequencing and re-sequencing opportunity for population individuals of genetic crosses and breeding lines. This helps to precisely identify and link genetic variations to the phenotypic expressions, taking into account the rare and private allelic variations that are abundant in crop line population or germplasm resources [26,53,54]. Furthermore, the availability of SNP marker collections and automated genotyping platforms provided a better genome converge to perform genome-wide genotype-to-phenotype associations (GWAS) [11,37].…”

Section: Genomics-assisted Selection or Genomic Selectionmentioning

confidence: 99%

“…Furthermore, the availability of SNP marker collections and automated genotyping platforms provided a better genome converge to perform genome-wide genotype-to-phenotype associations (GWAS) [11,37]. Also, when whole-genome sequences are not available and SNP markers are present in a limited number, the breeders using GBS and HTS platforms can readily genotype their mapping population and can provide genomic selections for the targeted crops of interest [23,26,54]. Although it was first applied for animal breeding [55], recently genomic selection has been successfully applied to a number of plant species [56][57][58][59][60][61][62], including studies using GBS in the context of genomic selection [26].…”

Section: Genomics-assisted Selection or Genomic Selectionmentioning

confidence: 99%

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Genomics Era for Plants and Crop Species – Advances Made and Needed Tasks Ahead

Abdurakhmonov¹

2016

Plant Genomics

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Historically, unintentional plant selection and subsequent crop domestication, coupled with the need and desire to get more food and feed products, have resulted in the continuous development of plant breeding and genetics efforts. The progress made toward this goal elucidated plant genome compositions and led to decoding the full DNA sequences of plant genomes controlling the entire plant life. Plant genomics aims to develop highthroughput genome-wide-scale technologies, tools, and methodologies to elucidate the basics of genetic traits/characteristics, genetic diversities, and by-product production; to understand the phenotypic development throughout plant ontogenesis with genetic by environmental interactions; to map important loci in the genome; and to accelerate crop improvement. Plant genomics research efforts have continuously increased in the past 30 years due to the availability of cost-effective, high-throughput DNA sequencing platforms that resulted in fully sequenced 100 plant genomes with broad implications for every aspect of plant biology research and application. These technological advances, however, also have generated many unexpected challenges and grand tasks ahead. In this introductory chapter, I aimed briefly to summarize some advances made in plant genomics studies in the past three decades, plant genome sequencing efforts, current state-of-the-art technological developments of genomics era, and some of current grand challenges and needed tasks ahead in the genomics and post-genomics era. I also highlighted the related book chapters contributed by different authors in this book.

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Section: Genomics-assisted Selection or Genomic Selectionmentioning

confidence: 99%

Section: Genomics-assisted Selection or Genomic Selectionmentioning

confidence: 99%

Genomics Era for Plants and Crop Species – Advances Made and Needed Tasks Ahead

Abdurakhmonov¹

2016

Plant Genomics

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“…A marker-assisted breeding program requires simple but robust molecular assays that benefit from economies of scale. Kompetitive allele-specific PCR (KASPar) genotyping assay is considered as an ideal approach to hasten the breeding processes through rapid genotyping of thousands of samples at very low error rates ( Chen et al, 2010 ; Kumpatla et al, 2012 ). In this study, we report the development of KASPar assay for high-throughput genotyping of erucic acid content.…”

Section: Introductionmentioning

confidence: 99%

Development and Validation of Kompetitive Allele-Specific PCR Assays for Erucic Acid Content in Indian Mustard [Brassica juncea (L.) Czern and Coss.]

Gill

Kaur

et al. 2021

Front. Plant Sci.

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Brassica juncea L. is the most widely cultivated oilseed crop in Indian subcontinent. Its seeds contain oil with very high concentration of erucic acid (≈50%). Of late, there is increasing emphasis on the development of low erucic acid varieties because of reported association of the consumption of high erucic acid oil with cardiac lipidosis. Erucic acid is synthesized from oleic acid by an elongation process involving two cycles of four sequential steps. Of which, the first step is catalyzed by β-ketoacyl-CoA synthase (KCS) encoded by the fatty acid elongase 1 (FAE1) gene in Brassica. Mutations in the coding region of the FAE1 lead to the loss of KCS activity and consequently a drastic reduction of erucic acid in the seeds. Molecular markers have been developed on the basis of variation available in the coding or promoter region(s) of the FAE1. However, majority of these markers are not breeder friendly and are rarely used in the breeding programs. Present studies were planned to develop robust kompetitive allele-specific PCR (KASPar) assays with high throughput and economics of scale. We first cloned and sequenced FAE1.1 and FAE1.2 from high and low erucic acid (<2%) genotypes of B. juncea (AABB) and its progenitor species, B. rapa (AA) and B. nigra (BB). Sequence comparisons of FAE1.1 and FAE1.2 genes for low and high erucic acid genotypes revealed single nucleotide polymorphisms (SNPs) at 8 and 3 positions. Of these, three SNPs for FAE1.1 and one SNPs for FAE1.2 produced missense mutations, leading to amino acid modifications and inactivation of KCS enzyme. We used SNPs at positions 735 and 1,476 for genes FAE1.1 and FAE1.2, respectively, to develop KASPar assays. These markers were validated on a collection of diverse genotypes and a segregating backcross progeny. KASPar assays developed in this study will be useful for marker-assisted breeding, as these can track recessive alleles in their heterozygous state with high reproducibility.

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Apple Rootstocks

Marini

Fazio²

2018

Horticultural Reviews

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Genomics-Assisted Plant Breeding in the 21st Century: Technological Advances and Progress

Cited by 16 publications

References 178 publications

Genomics Era for Plants and Crop Species – Advances Made and Needed Tasks Ahead

Genomics Era for Plants and Crop Species – Advances Made and Needed Tasks Ahead

Development and Validation of Kompetitive Allele-Specific PCR Assays for Erucic Acid Content in Indian Mustard [Brassica juncea (L.) Czern and Coss.]

Apple Rootstocks

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