Abstract
Identification of quantitative trait loci (QTLs) governing morphologically important traits enables to comprehend their potential genetic mechanisms in the genetic breeding program. In this study, we used 210 F2 populations derived from a cross between two radish inbred lines (Raphanus sativus) “835” and “B2,” including 258 SSR markers were used to detect QTLs for 11 morphological traits that related to whole plant, leaf, and root yield in 3 years of replicated field test. Total 55 QTLs were detected which were distributed on each linkage group of the Raphanus genome. Individual QTLs accounted for 2.69–12.6 of the LOD value, and 0.82–16.25% of phenotypic variation. Several genomic regions have multiple traits that clustered together, suggested the existence of pleiotropy linkage. Synteny analysis of the QTL regions with A. thaliana genome selected orthologous genes in radish. InDels and SNPs in the parental lines were detected in those regions by Illumina genome sequence. Five identified candidate gene-based markers were validated by co-mapping with underlying QTLs affecting different traits. Semi-quantitative reverse transcriptase PCR analysis showed the different expression levels of these five genes in parental lines. In addition, comparative QTL analysis with B. rapa revealed six common QTL regions and four key major evolutionarily conserved crucifer blocks (J, U, R, and W) harboring QTL for morphological traits. The QTL positions identified in this study will provide a valuable resource for identifying more functional genes when whole radish genome sequence is released. Candidate genes identified in this study that co-localized in QTL regions are expected to facilitate in radish breeding programs.
Highlights
Radish (Raphanus sativus; 2n = 18) is a diploid plant with estimated genome size of 530 Mb (Marie and Brown, 1993)
LG5 and LG7 were joined named as LG5, in addition, LG8 was swapped as LG7 and more over we have got a new linkage group including 12 reference markers which was determined as LG8. (Figure 1, Supplementary Table 1)
Because the F2:3 population consisted of genetic information from both heterozygous and homozygous individuals, it allowed the exploration of advantageous QTL/genes for radish breeding improvements
Summary
Radish (Raphanus sativus; 2n = 18) is a diploid plant with estimated genome size of 530 Mb (Marie and Brown, 1993). It is an economically important crop grown for its edible root and leaves. The species belongs to Brassicaceae, a family that includes several other important crops, such as Chinese cabbage, cabbage, and oilseed. Among these crops of Brassicaceae, radish is perhaps the least characterized in terms of the genetics basic that govern morphological yield traits. Morphological traits are key contributors to the storage root yield and quality
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