Effect of Chromosomal Localization of NGS-Based Markers on Their Applicability for Analyzing Genetic Variation and Population Structure of Hexaploid Triticale
International Journal of Molecular Sciences, ISSN: 1422-0067, Vol: 25, Issue: 17
2024
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IJMS, Vol. 25, Pages 9568: Effect of Chromosomal Localization of NGS-Based Markers on Their Applicability for Analyzing Genetic Variation and Population Structure of Hexaploid Triticale
IJMS, Vol. 25, Pages 9568: Effect of Chromosomal Localization of NGS-Based Markers on Their Applicability for Analyzing Genetic Variation and Population Structure of Hexaploid Triticale
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Data from University of Life Sciences in Lublin Provide New Insights into Genetics (Effect of Chromosomal Localization of NGS-Based Markers on Their Applicability for Analyzing Genetic Variation and Population Structure of Hexaploid Triticale)
2024 SEP 20 (NewsRx) -- By a News Reporter-Staff News Editor at NewsRx Life Science Daily -- Investigators discuss new findings in genetics. According to
Article Description
This study aimed to determine whether using DNA-based markers assigned to individual chromosomes would detect the genetic structures of 446 winter triticale forms originating from two breeding companies more effectively than using the entire pool of markers. After filtering for quality control parameters, 6380 codominant single nucleotide polymorphisms (SNPs) markers and 17,490 dominant diversity array technology (silicoDArT) markers were considered for analysis. The mean polymorphic information content (PIC) values varied depending on the chromosomes and ranged from 0.30 (2R) to 0.43 (7A) for the SNPs and from 0.28 (2A) to 0.35 (6R) for the silicoDArTs. The highest correlation of genetic distance (GD) matrices based on SNP markers was observed among the 5B–5R (0.642), 5B–7B (0.626), and 5A–5R (0.605) chromosomes. When silicoDArTs were used for the analysis, the strongest correlations were found between 5B–5R (0.732) and 2B–5B (0.718). A Bayesian analysis showed that SNPs (total marker pool) allowed for the identification of a more complex structure (K = 4, ΔK = 2460.2) than the analysis based on silicoDArTs (K = 2, ΔK = 128). Triticale lines formed into groups, ranging from two (most of the chromosomes) to four (7A) groups depending on the analyzed chromosome when SNP markers were used for analysis. Linkage disequilibrium (LD) varied among individual chromosomes, ranging from 0.031 for 1A to 0.228 for 7R.
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