Topic
Molecular breeding
About: Molecular breeding is a research topic. Over the lifetime, 2120 publications have been published within this topic receiving 56908 citations.
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01 Jan 2015
TL;DR: Progress in genome sequencing technology and its application to plant breeding is reviewed and the use of epigenome analysis to interpret phenotypic variations that cannot be explained by simple genetics based on the underlying DNA sequence alone, but rather by epigenetically-controlled mechanisms is described.
Abstract: Since the Arabidopsis genome was sequenced, hundreds of plant genomes have either been sequenced or are in sequencing progress. Reference genome sequences and large-scale genome sequencing technologies have initiated a new era in molecular breeding. The field of genomics is progressing rapidly and has already provided invaluable practical products for plant molecular breeding. Here, we review progress in genome sequencing technology and its application to plant breeding. We introduce various genomics tools and discuss how next-generation genome sequencing and genotyping technologies have been applied to high-throughput molecular breeding. We also describe the use of epigenome analysis to interpret phenotypic variations that cannot be explained by simple genetics based on the underlying DNA sequence alone, but rather by epigenetically-controlled mechanisms.
13 citations
TL;DR: Genomic information from this study endows with valuable resources for perceptive rice landrace structure and can also facilitate sequencing-based molecular breeding.
Abstract: Rice landraces are vital genetic resources for agronomic and quality traits but the undeniable collection of Kerala landraces remains poorly delineated. To effectively conserve, manage, and use these resources, understanding the genomic structure of germplasm is essential. Genotyping by sequencing (GBS) enables identification of an immense number of single nucleotide polymorphism (SNP) and insertion deletion (InDel) from 96 rice germplasm. In the present study, a total of 16.9 × 107 reads were generated, and among that 16.3 × 107 reads were mapped to the indica reference genome. Exploring GBS data unfolded a wide genomic variations including 82,59,639 SNPs and 1,07,140 Indels. Both neighbor-joining tree and principal coordinate analysis with InDel markers revealed the selected germplasm in this study as highly diverse in structure. We assembled unmapped reads which were further employed for gene ontology analysis. These unmapped sequences that are generally expelled from subsequent studies of GBS data analysis may exist as an unexplored resort for several novel significant biological findings. The discovery of SNPs from the haplotyping results of GS3 and GIF1 genes provided insight into marker- assisted selection based on grain size and yield and can be utilized for rice yield improvement. To our knowledge, this is the first report on structural variation analysis using the GBS platform in rice landraces collected from Kerala. Genomic information from this study endows with valuable resources for perceptive rice landrace structure and can also facilitate sequencing-based molecular breeding.
13 citations
01 Jan 2014
TL;DR: The high level of linkage disequilibrium and the close genetic relationship present in barley breeding material allow the use of relatively small marker sets to test populations for Genomic Selection in barleybreeding and suggest that this method will be highly useful for barley breeding.
Abstract: Genomic Selection is the improvement of breeding populations by using genome-wide markers for selection. In this breeding method, a calibration population is simultaneously phenotyped for traits of interest and genotyped with a genome-wide set of markers. Then, a quantitative genetic model for genomic prediction is trained using both the phenotypic and genotypic data. In subsequent selection cycles, individuals from a breeding population are only genotyped with the same markers, and their genomic estimated breeding values (GEBV) are calculated with the statistical model. Individuals with a high GEBV are selected for the next cycle. Genomic Selection leads to significant cost savings and to an increased selection gain per time unit as costly and time-consuming phenotypic selection does not have to be performed in every selection cycle. Both simulations and empirical studies showed a high accuracy of genomic prediction in barley breeding populations. The high level of linkage disequilibrium and the close genetic relationship present in barley breeding material allow the use of relatively small marker sets to test populations for Genomic Selection in barley breeding and suggest that this method will be highly useful for barley breeding.
13 citations
TL;DR: Several approaches are being employed for developing rice varieties with increased yield potential, such as population improvement, ideotype breeding, heterosis breeding, wide hybridization, genetic engineering, and molecular breeding as mentioned in this paper.
Abstract: Rice is the most important food crop in the world. Major advances have occurred in rice production as a result of the wide-scale adoption of improved rice varieties. However, demand for rice in low-income countries continues to increase because of increases in the population of rice consumers and improvements in living standards. It is estimated that we will have to produce 50% more rice by 2050. To meet this challenge, we need rice varieties with higher yield potential. Several approaches are being employed for developing rice varieties with increased yield potential, such as population improvement, ideotype breeding, heterosis breeding, wide hybridization, genetic engineering, and molecular breeding.
13 citations
TL;DR: How integration of other methodologies including whole genome sequencing, proteomics, transcriptomics and metabolomics with plant exomics covers the areas which are left untouched with exomics alone is concluded and in the end how these integration will transform the future of crops is concluded.
Abstract: Molecular breeding has a crucial role in improvement of crops. Conventional breeding techniques have failed to ameliorate food production. Next generation sequencing has established new concepts of molecular breeding. Exome sequencing has proven to be a significant tool for assessing natural evolution in plants, studying host pathogen interactions and betterment of crop production as exons assist in interpretation of allelic variation with respect to their phenotype. This review covers the platforms for exome sequencing, next generation sequencing technologies that have revolutionized exome sequencing and led toward development of third generation sequencing. Also discussed in this review are the uses of these sequencing technologies to improve wheat, rice and cotton yield and how these technologies are used in exploring the biodiversity of crops, providing better understanding of plant-host pathogen interaction and assessing the process of natural evolution in crops and it also covers how exome sequencing identifies the gene pool involved in symbiotic and other co-existential systems. Furthermore, we conclude how integration of other methodologies including whole genome sequencing, proteomics, transcriptomics and metabolomics with plant exomics covers the areas which are left untouched with exomics alone and in the end how these integration will transform the future of crops.
13 citations