SNP-based analysis of genetic diversity in anther-derived rice by whole genome sequencing

Abstract

Background: Anther culture has advantage to obtain a homozygous progeny by induced doubling of haploid chromosomes and to improve selection efficiency for invaluable agronomical traits. Therefore, anther culturing is widely utilized to breed new varieties and to induce genetic variations in several crops including rice. Genome sequencing technologies allow the detection of a massive number of DNA polymorphism such as SNPs and Indels between closely related cultivars. These DNA polymorphisms permit the rapid identification of genetic diversity among cultivars and genomic locations of heritable traits. To estimate sequence diversity derived from anther culturing, we performed whole-genome resequencing of five Korean rice accessions, including three anther culture lines (BLB, HY-04 and HY-08), their progenitor cultivar (Hwayeong), and an additional japonica cultivar (Dongjin).

Characterization of disease resistance genes in the Brassica napus pangenome reveals significant structural variation

“…For instance, in Arabidopsis, R-genes are known to accumulate large numbers of non-synonymous SNPs, producing new allelic variants of R-genes (Bakker et al, 2006). A higher proportion of nonsynonymous SNPs have been reported in other plants, for instance 56% non-synonymous SNPs in oil palm (Pootakham et al, 2015), 57% in sorghum (Zheng et al, 2011) and 54%-57% in rice (Jeong et al, 2013;Subbaiyan et al, 2012).…”

“…Several QTL responsible for quantitative resistance have been identified in B. napus cultivars (Huang et al, 2016;Jestin et al, 2011;Larkan et al, 2016;Raman et al, 2012b). We identified 106 RGA candidates and 688 SNPs within QTL regions associated with blackleg resistance.…”

Analisis Molekuler dan Uji Daya Hasil Galur-Galur Pup1

“…Teknologi ini telah diaplikasikan pada tanaman padi hasil kultur anter (Jeong et al, 2013) dan untuk membedakan keragaman di antara varietas/padi lokal di India (Choudhury et al, 2014;Singh et al, 2013). Di Indonesia, aplikasi marka SNP untuk analisis keragaman genetik telah dilakukan (Utami et al, 2013(Utami et al, , 2014.…”

Plant exomics: Concepts, applications and methodologies in crop improvement

“…68 By comparing the 2 genomes of japonica rice cultivar that are Nipponbare and Koshihikari 69 about 67,051 Single Nucleotide Polymorphisms have been recognized. 68 Next generation sequencing has been used to sequence 10 genomes of Oryza genus by using 454 Life Sequencing platforms. The complete sequence of chromosome arm of Oryza barthii has been accomplished.…”

“…The results provide genetic analysis of BGR resistance in rice and thus this trait could be targeted for marker-assisted selection for rice improvement. 73 Culture of anther studies has been used to attain a homozygous progeny by inducing the doubling of 'n' chromosomes in order to enhance agronomical traits selection, amount of DNA polymorphism including SNPs and Indels among related cultivars has been detected by high-throughput sequencer, Jeong et al 68 estimated sequence variety resulting from anther culturing by performing WGRS of 5 Korean including 3 anther culture lines, their progenitor Hwayeong cultivar, and Dongjin japonica cultivar. It was found that the genetic difference amid progenies resulting from anther culture and their parent cultivar was a result owing to somaclonal variations.…”