scholarly journals Whole Genome Resequencing from Bulked Populations as a Rapid QTL and Gene Identification Method in Rice

2018 ◽  
Vol 19 (12) ◽  
pp. 4000 ◽  
Author(s):  
Workie Zegeye ◽  
Yingxin Zhang ◽  
Liyong Cao ◽  
Shihua Cheng
Keyword(s):  
Agronomic Traits ◽  
Genetic Material ◽  
Gene Isolation ◽  
Causative Mutation ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Crop Genetics ◽  
Genomic Study ◽  
Whole Genome Resequencing ◽  
Or Genes

Most Quantitative Trait Loci (QTL) and gene isolation approaches, such as positional- or map-based cloning, are time-consuming and low-throughput methods. Understanding and detecting the genetic material that controls a phenotype is a key means to functionally analyzing genes as well as to enhance crop agronomic traits. In this regard, high-throughput technologies have great prospects for changing the paradigms of DNA marker revealing, genotyping, and for discovering crop genetics and genomic study. Bulk segregant analysis, based on whole genome resequencing approaches, permits the rapid isolation of the genes or QTL responsible for the causative mutation of the phenotypes. MutMap, MutMap Gap, MutMap+, modified MutMap, and QTL-seq methods are among those approaches that have been confirmed to be fruitful gene mapping approaches for crop plants, such as rice, irrespective of whether the characters are determined by polygenes. As a result, in the present study we reviewed the progress made by all these methods to identify QTL or genes in rice.

scholarly journals Whole-genome resequencing of 292 pigeonpea accessions identifies genomic regions associated with domestication and agronomic traits

2017 ◽  
Vol 49 (7) ◽  
pp. 1082-1088 ◽  
Author(s):  
Rajeev K Varshney ◽  
Rachit K Saxena ◽  
Hari D Upadhyaya ◽  
Aamir W Khan ◽  
Yue Yu ◽  
...  
Keyword(s):  
Agronomic Traits ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Whole Genome Resequencing ◽  
Genomic Regions

scholarly journals Seeing the Forest through the (Phylogenetic) Trees: Functional Characterisation of Grapevine Terpene Synthase (VviTPS) Paralogues and Orthologues

Plants ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 1520
Author(s):  
Samuel J. Smit ◽  
Melané A. Vivier ◽  
Philip R. Young
Keyword(s):  
Phylogenetic Trees ◽  
Reference Genome ◽  
Gene Isolation ◽  
Terpene Synthase ◽  
Sequence Information ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Volatile Analysis ◽  
Functional Characterisation ◽  
Whole Genome Resequencing

Gene families involved in specialised metabolism play a key role in a myriad of ecophysiological and biochemical functions. The Vitis vinifera sesquiterpene synthases represent the largest subfamily of grapevine terpene synthase (VviTPS) genes and are important volatile metabolites for wine flavour and aroma, as well as ecophysiological interactions. The functional characterisation of VviTPS genes is complicated by a reliance on a single reference genome that greatly underrepresents this large gene family, exacerbated by extensive duplications and paralogy. The recent release of multiple phased diploid grapevine genomes, as well as extensive whole-genome resequencing efforts, provide a wealth of new sequence information that can be utilised to overcome the limitations of the reference genome. A large cluster of sesquiterpene synthases, localised to chromosome 18, was explored by means of comparative sequence analyses using the publicly available grapevine reference genome, three PacBio phased diploid genomes and whole-genome resequencing data from multiple genotypes. Two genes, VviTPS04 and -10, were identified as putative paralogues and/or allelic variants. Subsequent gene isolation from multiple grapevine genotypes and characterisation by means of a heterologous in planta expression and volatile analysis resulted in the identification of genotype-specific structural variations and polymorphisms that impact the gene function. These results present novel insight into how grapevine domestication likely shaped the VviTPS landscape to result in genotype-specific functions.

scholarly journals Morphoagronomic characterization and whole-genome resequencing of eight highly diverse wild and weedy S. pimpinellifolium and S. lycopersicum var. cerasiforme accessions used for the first interspecific tomato MAGIC population

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Pietro Gramazio ◽  
Leandro Pereira-Dias ◽  
Santiago Vilanova ◽  
Jaime Prohens ◽  
Salvador Soler ◽  
...  
Keyword(s):  
Agronomic Traits ◽  
Functional Characterization ◽  
Principal Component ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Genomic Studies ◽  
History Of ◽  
Whole Genome Resequencing ◽  
Magic Population

Abstract The wild Solanum pimpinellifolium (SP) and the weedy S. lycopersicum var. cerasiforme (SLC) are largely unexploited genetic reservoirs easily accessible to breeders, as they are fully cross-compatible with cultivated tomato (S. lycopersicum var. lycopersicum). We performed a comprehensive morphological and genomic characterization of four wild SP and four weedy SLC accessions, selected to maximize the range of variation of both taxa. These eight accessions are the founders of the first tomato interspecific multi-parent advanced generation inter-cross (MAGIC) population. The morphoagronomic characterization was carried out with 39 descriptors to assess plant, inflorescence, fruit and agronomic traits, revealing the broad range of diversity captured. Part of the morphological variation observed in SP was likely associated to the adaptation of the accessions to different environments, while in the case of SLC to both human activity and adaptation to the environment. Whole-genome resequencing of the eight accessions revealed over 12 million variants, ranging from 1.2 to 1.9 million variants in SLC and from 3.1 to 4.8 million in SP, being 46.3% of them (4,897,803) private variants. The genetic principal component analysis also confirmed the high diversity of SP and the complex evolutionary history of SLC. This was also reflected in the analysis of the potential footprint of common ancestors or old introgressions identified within and between the two taxa. The functional characterization of the variants revealed a significative enrichment of GO terms related to changes in cell walls that would have been negatively selected during domestication and breeding. The comprehensive morphoagronomic and genetic characterization of these accessions will be of great relevance for the genetic analysis of the first interspecific MAGIC population of tomato and provides valuable knowledge and tools to the tomato community for genetic and genomic studies and for breeding purposes.

scholarly journals Whole genome resequencing and custom genotyping unveil clonal lineages in ‘Malbec’ grapevines (Vitis vinifera L.)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Luciano Calderón ◽  
Nuria Mauri ◽  
Claudio Muñoz ◽  
Pablo Carbonell-Bejerano ◽  
Laura Bree ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Somatic Mutations ◽  
Clonal Propagation ◽  
Variant Calling ◽  
Vitis Vinifera L ◽  
Whole Genome ◽  
Single Nucleotide Variants ◽  
Genome Resequencing ◽  
Diversity Pattern ◽  
Whole Genome Resequencing

AbstractGrapevine cultivars are clonally propagated to preserve their varietal attributes. However, genetic variations accumulate due to the occurrence of somatic mutations. This process is anthropically influenced through plant transportation, clonal propagation and selection. Malbec is a cultivar that is well-appreciated for the elaboration of red wine. It originated in Southwestern France and was introduced in Argentina during the 1850s. In order to study the clonal genetic diversity of Malbec grapevines, we generated whole-genome resequencing data for four accessions with different clonal propagation records. A stringent variant calling procedure was established to identify reliable polymorphisms among the analyzed accessions. The latter procedure retrieved 941 single nucleotide variants (SNVs). A reduced set of the detected SNVs was corroborated through Sanger sequencing, and employed to custom-design a genotyping experiment. We successfully genotyped 214 Malbec accessions using 41 SNVs, and identified 14 genotypes that clustered in two genetically divergent clonal lineages. These lineages were associated with the time span of clonal propagation of the analyzed accessions in Argentina and Europe. Our results show the usefulness of this approach for the study of the scarce intra-cultivar genetic diversity in grapevines. We also provide evidence on how human actions might have driven the accumulation of different somatic mutations, ultimately shaping the Malbec genetic diversity pattern.

scholarly journals Whole genome resequencing of black Angus and Holstein cattle for SNP and CNV discovery

BMC Genomics ◽  
2011 ◽  
Vol 12 (1) ◽  
Author(s):  
Paul Stothard ◽  
Jung-Woo Choi ◽  
Urmila Basu ◽  
Jennifer M Sumner-Thomson ◽  
Yan Meng ◽  
...  
Keyword(s):  
Holstein Cattle ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Whole Genome Resequencing
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