Development of chloroplast derived SSR markers for genus Allium and their characterization in the allies for genetic improvement of alliums

Abstract

Alliums are the most popular for their culinary usage and nutraceutical benefits. Their productions are greatly affected by the multiple biotic and abiotic stresses. Poor characterizations of genetic resources are the major bottleneck in genetic improvement of alliums. Chloroplast derived simple sequence repeat (cpSSR) have recently gained much popularity due to their maternal inheritance and low recombination along with their hypervariable nature. In this study, 22 chloroplast-derived SSR markers were produced from chloroplast genomes of A. cepa and A. sativum. Repeat comparison revealed tri nucleotide repeats were in higher proportion (50%) compared to other repeat motifs. The number of alleles ranged from 2 to 4, heterozygosity from 0.009 to 0.540, and PIC from 0.007 to 0.427. The polymorphism survey and clustering of twenty-two cpSSR markers of twenty-five alliums, lead to three groups (groups I, II, and III), indicated the usefulness of these cpSSR markers. This demonstrated that cultivated A. cepa and A. sativum belong to different groups II than most wild alliums, confirming the usefulness of the AccpSSR and AscpSSR markers that will allow introduction of desirable biotic and abiotic tolerance traits from various wild alliums to selected cultivated alliums. In addition, these cpSSRs were validated in 79 alliums, divided them into three groups using Jaccard dissimilarity and Bayesian model-based structure analysis. Subsequent clustering allowed us to identify diverse alliums, for constructing core collection of germplasm resource. The study will be useful for molecular breeding and genomic selection based crop improvement.

Development of chloroplast derived SSR markers for genus Allium and their characterization in the allies for genetic improvement of Alliums

“…Many chloroplast genes regulate the transcription of various nuclear genes, and play important role in withstanding various biotic and abiotic stresses (Jayaswall et al2016 andWang et al2016). The widely consumed vegetables Allium cepa and Allium sativum, which are grown all over the world, had seen an increase in the production and productivity.But various biotic and abiotic stresses are reducing yield of cultivated alliums (Choi et al 2020).Therefore, introgression of many desirable genes/traits/QTLs controlling adverse effect of various biotic and abiotic stresses is need of the hour.Despite this, no cpSSR maker resources of Allium cepa and Allium sativum have been reported yet except our previous study where we mined 15cpSSR markers from Allium paradoxum (Jayaswall et al 2021).In alliums, cpSSR markers may be utilized for genetic identi cation, characterization, and introgression of desirable traits through linked molecular markers (Parida et al2010).Therefore, nding functionally appropriate and validated polymorphic-cross transferrable cpSSR markers will help in evolutionary studies and trait introgression (Sharma et al 2020b).…”

“…Based on speci ed criteria, a total of twenty-two cpSSRs were mined and tested for ampli cation success in 25 alliums. Previously, 15 cpSSR were identi ed in the wild allium species (Jayaswall et al 2021), but the current study represents the rst report of development of chloroplast SSR markers in cultivated alliums i.e.,Allium cepa and Allium sativum.In comparison to other types of chloroplast dwelling SSR repeats; Allium cepa and Allium sativum mainly include tri-nucleotide repeats (50%) . This prevalence of tri-nucleotide repeats could be related to genomic selection against frameshift mutations in the coding genes which is similar to the protein coding regions of the genome (Varshney et al 2005, Metzgar et al 2000.…”

“…The chloroplast genomes of onion and garlic were recently sequenced by using various sequencing technologies (Von Kohn et al 2013;Filyushin et al 2016) that provides an opportunity for the development of cpSSR markers resources in onion and garlic. Previously, Jayaswall et al (2021) mined 15 cpSSR markers from Allium paradoxum for genotyping 18 alliums. Therefore, to understand the polymorphism and cross-transferabilities of cultivated alliums derived 22 novel cpSSR markers in 25 diverse alliums and to decipher genetic diversity and population structure of 79 alliums in this study, chloroplast genome sequence of A.cepa(onion)and A. sativum(garlic)were used to develop cpSSR markers.…”