Genetic diversity analysis using DArTseq and SNP markers in populations of Aegilops species from Azerbaijan

Abstract Flax is an important oil and fibre crop grown in Northern Europe, Canada, India, and China. The development of molecular markers has accelerated the process of flax molecular breeding and has improved yield and quality. Presently, simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers in the whole genome have been developed for flax. However, the development of flax insertion/deletion (InDel) markers has not been reported. A total of 17,110 InDel markers were identified by comparing whole-genome re-sequencing data of two accessions (87-3 and 84-3) with the flax reference genome. The length of InDels ranged from 1–277 bp, with 1–15 bp accounting for the highest rate (95.55%). The most common InDels were in the form of single nucleotide (8840), dinucleotide (3700), and trinucleotide (1349), and chromosome 2 (1505) showed the highest number of InDels among flax chromosomes, while chromosome 10 (913) presented with the lowest number. From 17,110 InDel markers, 90 primers that were evenly distributed in the flax genome were selected. Thirty-two pairs of polymorphic primers were detected in two flax accessions, and the polymorphism rate was 40.70%. Furthermore, genetic diversity analysis, population structure and principal component analyse (PCA) divided 69 flax accessions into two categories, namely oilseed flax and fibre flax using 32 pairs of polymorphic primers. Additionally, correlation analysis showed that InDel-26 and InDel-81 were associated with oil content traits, and two candidate genes (lus10031535 and lus10025284) tightly linked to InDel-26 or InDel-81, might be involved in flax lipid biosynthesis and lipid metabolism. This study is the first to develop InDel markers based on re-sequencing in flax and clustered the markers into two well-separated groups for oil and fibre. The results demonstrated that InDel markers developed herein could be used for flax germplasm identification, genetic diversity analysis, and molecular marker-assisted breeding.

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Molecular diversity analysis of genotypes from four Aegilops species based on retrotransposon–microsatellite amplified polymorphism (REMAP) markers

Cereal Research Communications ◽

10.1007/s42976-020-00086-1 ◽

2020 ◽

Author(s):

Justyna Leśniowska-Nowak ◽

Sylwia Okoń ◽

Aleksandra Wieremczuk

Keyword(s):

Genetic Diversity ◽

Molecular Diversity ◽

Crop Improvement ◽

Diversity Analysis ◽

Aegilops Species ◽

Powerful Method ◽

High Genetic Diversity ◽

Breeding Programs ◽

Genetic Diversity Analysis ◽

Valuable Source

Abstract Genetic diversity analysis is an important tool in crop improvement. Species with high genetic diversity are a valuable source of variation used in breeding programs. The aim of this study was to assess the genetic diversity of four species belonging to the genus Aegilops, which are often used to expand the genetic variability of wheat and triticale. Forty-five genotypes belonging to the genus Aegilops were investigated. Within- and among-species genetic diversity was calculated based on REMAP (retrotransposon–microsatellite amplified polymorphism) molecular markers. Obtained results showed that REMAP markers are a powerful method for genetic diversity analysis, which produces a high number of polymorphic bands (96.09% of total bands were polymorphic). Among tested genotypes, Ae. crassa and Ae. vavilovii showed the highest genetic diversity and should be chosen as a valuable source of genetic variation.

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Development of SNP markers and their application for genetic diversity analysis in the oil palm (Elaeis guineensis)

Genetics and Molecular Research ◽

10.4238/2015.october.9.9 ◽

2015 ◽

Vol 14 (4) ◽

pp. 12205-12216 ◽

Cited By ~ 7

Author(s):

P.W. Ong ◽

I. Maizura ◽

N.A.P. Abdullah ◽

M.Y. Rafii ◽

L.C.L. Ooi ◽

...

Keyword(s):

Genetic Diversity ◽

Oil Palm ◽

Elaeis Guineensis ◽

Snp Markers ◽

Diversity Analysis ◽

Genetic Diversity Analysis

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GENETIC DIVERSITY ANALYSIS OF DOMESTICATED WHEAT (Triticum aestivum L.) AND WILD WHEAT (Aegilops species)

Egyptian Journal of Genetics and Cytology ◽

10.21608/ejgc.2013.10455 ◽

2013 ◽

Vol 42 (1) ◽

pp. 21-36

Author(s):

N. ABDELSALAM ◽

REHAM ABD EL-AZEEM

Keyword(s):

Genetic Diversity ◽

Triticum Aestivum ◽

Triticum Aestivum L ◽

Diversity Analysis ◽

Aegilops Species ◽

Wild Wheat ◽

Genetic Diversity Analysis

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Genetic diversity analysis of Indonesian native chickens using SNP markers on the Z chromosome

The Journal of Animal Genetics ◽

10.5924/abgri.39.49 ◽

2011 ◽

Vol 39 (2) ◽

pp. 49-53 ◽

Cited By ~ 1

Author(s):

Riztyan ◽

Nyoman SUTHAMA ◽

Sri Murni ARDININGSASI ◽

Takeshi SHIMOGIRI ◽

Kotaro KAWABE ◽

...

Keyword(s):

Genetic Diversity ◽

Snp Markers ◽

Z Chromosome ◽

Diversity Analysis ◽

Genetic Diversity Analysis ◽

Native Chickens

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Development and Application of Novel InDel Markers in Flax (Linum usitatissimum L.) Through Whole-Genome Re-Sequencing

10.21203/rs.3.rs-700179/v1 ◽

2021 ◽

Author(s):

Hui Jiang ◽

Gen Pan ◽

Touming Liu ◽

Li Chang ◽

Siqi Huang ◽

...

Keyword(s):

Genetic Diversity ◽

Principal Component ◽

Snp Markers ◽

Diversity Analysis ◽

Whole Genome ◽

Chromosome 2 ◽

Sequencing Data ◽

Single Nucleotide ◽

Genetic Diversity Analysis ◽

Indel Markers

Abstract Flax is an important oil and fibre crop grown in Northern Europe, Canada, India, and China. The development of molecular markers has accelerated the process of flax molecular breeding and has improved yield and quality. Presently, simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers in the whole genome have been developed for flax. However, the development of flax insertion/deletion (InDel) markers has not been reported. A total of 17,110 InDel markers were identified by comparing whole-genome re-sequencing data of two accessions (87 − 3 and 84 − 3) with the flax reference genome. The length of InDels ranged from 1–277 bp, with 1–15 bp accounting for the highest rate (95.55%). The most common InDels were in the form of single nucleotide (8840), dinucleotide (3700), and trinucleotide (1349), and chromosome 2 (1505) showed the highest number of InDels among flax chromosomes, while chromosome 10 (913) presented with the lowest number. From 17,110 InDel markers, 90 primers that were evenly distributed in the flax genome were selected. Thirty-two pairs of polymorphic primers were detected in two flax accessions, and the polymorphism rate was 40.70%. Furthermore, genetic diversity analysis, population structure and principal component analyse (PCA) divided 69 flax accessions into two categories, namely oilseed flax and fibre flax using 32 pairs of polymorphic primers. Additionally, correlation analysis showed that InDel-26 and InDel-81 were associated with oil content traits, and two candidate genes (lus10031535 and lus10025284) tightly linked to InDel-26 or InDel-81, might be involved in flax lipid biosynthesis and lipid metabolism. This study is the first to develop InDel markers based on re-sequencing in flax and clustered the markers into two well-separated groups for oil and fibre. The results demonstrated that InDel markers developed herein could be used for flax germplasm identification, genetic diversity analysis, and molecular marker-assisted breeding.

Download Full-text