SSR marker variations in Brassica species provide insight into the origin and evolution of Brassica amphidiploids

Thakur, Ajay Kumar; Singh, K. H.; Singh, Lal; Nanjundan, J.; Yasin, Jeshima Khan; Singh, Dhiraj

doi:10.1186/s41065-017-0041-5

Cited by 45 publications

(38 citation statements)

References 25 publications

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“…The frequent mutations in SSR regions are easily to alter the number of repeats, result in a higher degree of polymorphism. Because of these characteristics, SSRs have become important molecular markers for a wide range of applications [43,44]. In compliance with other similar studies [32,45], we detected the perfect SSRs longer than 8 bp because SSRs of 8 bp or longer are prone to slip-strand mispairing, which is thought to be the primary mutational mechanism causing their high level of polymorphism.…”

Section: Repeat Sequence Analysis Of N Cadamba Chloroplast Genomesupporting

confidence: 88%

The complete chloroplast genome of the miracle treeNeolamarckia cadambaand its comparison in Rubiaceae family

Deng

Ouyang

et al. 2018

Biotechnology & Biotechnological Equipment

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Neolamarckia cadamba is a miracle tree species with considerable economic potential used as a timber wood and traditional medicine resource in South and Southeast Asia. To better understand the molecular basis of its chloroplast biology, we sequenced and characterised the complete chloroplast genome using Illumina pair-end sequencing. The analysis showed a chloroplast genome size of 154,999 bp in length, harbouring a pair of inverted repeats (IRs) of 25,634 bp separated by a large single copy (LSC) sequence of 85,880 bp and a small single copy (SSC) sequence of 17,851 bp. Of the 130 genes present, 96 were unique and 17 were duplicated in the IRs. The coding regions comprised 79 protein genes, 30 tRNA genes and 4 rRNA genes. In the protein-coding genes, nine genes contained one intron each, while another two genes comprised two introns. The overall GC content of the chloroplast genome was 37.6%. Simple sequence repeat (SSR) analysis revealed that most SSRs were A/T-rich, which contributed to the overall AT richness of the N. cadamba chloroplast genome. Additionally, fewer SSRs distributed in the protein-coding sequences compared to the non-coding regions, indicating an uneven distribution of SSRs within the chloroplast genome. A maximum likelihood phylogenetic analysis showed that N. cadamba was closely related to Morinda officinalis and Emmenopterys henryi, which belong to the Rubiaceae family. This complete chloroplast genome will offer valuable information for the development of highly variable DNA markers for future conservation, genetic engineering studies and variety selection of this miracle tree.

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Section: Repeat Sequence Analysis Of N Cadamba Chloroplast Genomesupporting

confidence: 88%

The complete chloroplast genome of the miracle treeNeolamarckia cadambaand its comparison in Rubiaceae family

Deng

Ouyang

et al. 2018

Biotechnology & Biotechnological Equipment

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“…In our knowledge, there are no specific molecular markers developed for other related species in the Sesamum genus. It has been demonstrated that SSR markers have a good transferability between species of the same genus or even in the same taxa ( Fan et al, 2013 ; Buso et al, 2016 ; Huang et al, 2016 ; Thakur et al, 2017 ). In sesame, Uncu et al (2015) uncovered a high rate of SSR marker transferability between the cultivated species S. indicum and the proposed wild ancestor species S. malabaricum .…”

Section: Discussionmentioning

confidence: 99%

Development of Highly Informative Genome-Wide Single Sequence Repeat Markers for Breeding Applications in Sesame and Construction of a Web Resource: SisatBase

Dossa

Liao

et al. 2017

Front. Plant Sci.

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The sequencing of the full nuclear genome of sesame (Sesamum indicum L.) provides the platform for functional analyses of genome components and their application in breeding programs. Although the importance of microsatellites markers or simple sequence repeats (SSR) in crop genotyping, genetics, and breeding applications is well established, only a little information exist concerning SSRs at the whole genome level in sesame. In addition, SSRs represent a suitable marker type for sesame molecular breeding in developing countries where it is mainly grown. In this study, we identified 138,194 genome-wide SSRs of which 76.5% were physically mapped onto the 13 pseudo-chromosomes. Among these SSRs, up to three primers pairs were supplied for 101,930 SSRs and used to in silico amplify the reference genome together with two newly sequenced sesame accessions. A total of 79,957 SSRs (78%) were polymorphic between the three genomes thereby suggesting their promising use in different genomics-assisted breeding applications. From these polymorphic SSRs, 23 were selected and validated to have high polymorphic potential in 48 sesame accessions from different growing areas of Africa. Furthermore, we have developed an online user-friendly database, SisatBase (http://www.sesame-bioinfo.org/SisatBase/), which provides free access to SSRs data as well as an integrated platform for functional analyses. Altogether, the reference SSR and SisatBase would serve as useful resources for genetic assessment, genomic studies, and breeding advancement in sesame, especially in developing countries.

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“…This suggests the need of understanding the B. oleracea gene pool for seed yield heterosis in B. napus canola hybrid. It has also been reported that genetic diversity in the C genome is lower than the A genome of B. napus (Bus et al, 2011;Delourme et al, 2013;Thakur et al, 2018); this enforce the need of increasing genetic diversity in the C genome of B. napus by introducing allelic diversity from B. oleracea-not only for increasing the level of heterosis in B. napus hybrid canola but also for continued improvement of the germplasm of this crop through breeding.…”

Section: Introductionmentioning

confidence: 99%

Potential of the C Genome of the Different Variants of Brassica oleracea for Heterosis in Spring B. napus Canola

et al. 2020

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The genetic base of Brassica napus canola need to be broadened for exploitation of heterosis at a greater level in the breeding of F 1 hybrid canola cultivars. In this study, we evaluated 228 inbred B. napus canola lines derived from six B. napus × B. oleracea interspecific crosses and following two breeding methods (F 2-and BC 1-derived lines) to understand the effect of the B. oleracea alleles on heterosis for different agronomic and seed quality traits. Test hybrids of the inbreds derived from crosses involving vars. botrytis (cauliflower), alboglabra (Chinese kale) and capitata (cabbage) cv. Badger Shipper, on an average, gave about 10% mid-parent heterosis (MPH), and about 67% of the test hybrids gave higher seed yield than the common B. napus parent indicating that B. oleracea alleles can contribute to heterosis for seed yield in spring B. napus canola hybrids. This was also evident from a positive correlation of the genetic distance of the inbred lines from the common B. napus parent with MPH for seed yield (r = 0.31) as well as with hybrid yield (r = 0.26). Almost no correlation was found between genetic distance and MPH for seed oil and protein content as well as with the performance of the test hybrids for these two traits. The occurrence of positive correlation between seed yield of the inbred lines and test hybrids suggested the importance of the genes exerting additive effect for high seed yield in the hybrids. Very little or almost no heterosis was found for the other agronomic traits as well as for seed oil and protein content. While comparing the two breeding methods, no significant difference was found for seed yield of the test hybrids or the level of MPH; however, the BC 1-derived inbred and test hybrid populations flowered and matured earlier and had longer grain-filling period than the F 2-derived population. Thus, the results suggested that the B. oleracea gene pool can be used in the breeding of spring B. napus canola to improve seed yield in hybrid cultivars.

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SSR marker variations in Brassica species provide insight into the origin and evolution of Brassica amphidiploids

Cited by 45 publications

References 25 publications

The complete chloroplast genome of the miracle treeNeolamarckia cadambaand its comparison in Rubiaceae family

The complete chloroplast genome of the miracle treeNeolamarckia cadambaand its comparison in Rubiaceae family

Development of Highly Informative Genome-Wide Single Sequence Repeat Markers for Breeding Applications in Sesame and Construction of a Web Resource: SisatBase

Potential of the C Genome of the Different Variants of Brassica oleracea for Heterosis in Spring B. napus Canola

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