Abstract
Simple sequence repeats (SSRs) are widely used as markers for the assessment of genetic diversity and marker-assisted breeding. In a previous study, two SSRs (GCA and CCA), were found in the genomic sequence of Larix (La) SCL6, which plays important roles in the growth and development of Larix kaempferi (Lamb.) Carr. In this study, we analyzed the polymorphisms of these two SSRs in the L. kaempferi population. We found that each SSR had five different polymorphisms, among which (GCA)7 and (CCA)7 were predominant. In addition, 12 haplotypes were detected, with (GCA)7(CCA)7 having the highest frequency. Furthermore, we detected the haplotypes of LaSCL6 in mature trees and their seeds and analyzed the relationships between parents and offspring. The expression patterns of five LaSCL6 alleles were analyzed and they showed balanced expression during vegetative development. Taken together, these findings not only provide more genetic information on LaSCL6, but also provide a candidate marker for genetic studies and breeding.
Highlights
Simple sequence repeats (SSRs) are a class of DNA sequences consisting of short, tandem-repeated motifs (1–6 bp in length) [1]
Some allelic variants show differential expression during plant growth and development [5,6,7]. Due to their advantages of being co-dominant, multi-allelic, reliable, Polymerase Chain Reaction (PCR)-based, and abundant in plant genomes [8], SSRs have been used as markers for the assessment of genetic diversity [9,10], genetic structure [11], parentage analyses [12], pedigree and mating system analyses [13], and marker-assisted breeding [14]
We identified the homologue of SCL6 in L. kaempferi, and we found two SSRs (GCA and containing the (GCA)6 or (CCA)) in the genomic sequence of LaSCL6 [22]
Summary
Simple sequence repeats (SSRs) are a class of DNA sequences consisting of short, tandem-repeated motifs (1–6 bp in length) [1]. SSR sequences are highly polymorphic, and their presence results in allelic variants with different frequencies at the population level [2,3,4]. Some allelic variants show differential expression during plant growth and development [5,6,7]. Due to their advantages of being co-dominant, multi-allelic, reliable, PCR-based, and abundant in plant genomes [8], SSRs have been used as markers for the assessment of genetic diversity [9,10], genetic structure [11], parentage analyses [12], pedigree and mating system analyses [13], and marker-assisted breeding [14]. SSRs have been used to investigate the pollen contamination rate and paternal contributions of
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