Genetic diversity analysis using RAPD and ISSR markers revealed discrete genetic makeup in relation to fibre and oil content in Linum usitatissimum L. genotypes

Kumari, Arpna; Paul, Satish; Sharma, Vikas

doi:10.1007/s13237-017-0206-7

Cited by 18 publications

(8 citation statements)

References 26 publications

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“…Molecular marker-based diversity is more precise and economic as it allows breeders to select unrelated individuals among thousands of genotypes within a short period of time which in turn reduces field workload by evaluating only unrelated genotypes. Different molecular marker techniques such as RAPD, AFLP, ISSR, SSR and IRAP has been used to assess the genetic diversity of flax germplasm [16][17][18][19][20][21][22]. The availability of a flax reference genome [23] has created the opportunity of discovery and exploitation of SNP markers, which are abundant and well distributed throughout the genome.…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity analysis of a flax (Linum usitatissimum L.) global collection

2020

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Background A sustainable breeding program requires a minimum level of germplasm diversity to provide varied options for the selection of new breeding lines. To maximize genetic gain of the North Dakota State University (NDSU) flax breeding program, we aimed to increase the genetic diversity of its parental stocks by incorporating diverse genotypes. For this purpose, we analyzed the genetic diversity, linkage disequilibrium, and population sub-structure of 350 globally-distributed flax genotypes with 6200 SNP markers. Results All the genotypes tested clustered into seven sub-populations (P1 to P7) based on the admixture model and the output of neighbor-joining (NJ) tree analysis and principal coordinate analysis were in line with that of structure analysis. The largest sub-population separation arose from a cluster of NDSU/American genotypes with Turkish and Asian genotypes. All sub-populations showed moderate genetic diversity (average H = 0.22 and I = 0.34). The pairwise F st comparison revealed a great degree of divergence ( F st > 0.25) between most of the combinations. A whole collection mantel test showed significant positive correlation (r = 0.30 and p < 0.01) between genetic and geographic distances, whereas it was non-significant for all sub-populations except P4 and P5 (r = 0.251, 0.349 respectively and p < 0.05). In the entire collection, the mean linkage disequilibrium was 0.03 and it decayed to its half maximum within < 21 kb distance. Conclusions To maximize genetic gain, hybridization between NDSU stock (P5) and Asian individuals (P6) are potentially the best option as genetic differentiation between them is highest ( F st > 0.50). In contrast, low genetic differentiation between P5 and P2 may enhance the accumulation of favorable alleles for oil and fiber upon crossing to develop dual purpose varieties. As each sub-population consists of many genotypes, a Neighbor-Joining tree and kinship matrix assist to identify distantly related genotypes. These results also inform genotyping decisions for future association mapping studies to ensure the identification of a sufficient number of molecular markers to tag all linkage blocks.

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Section: Introductionmentioning

confidence: 99%

Genetic diversity analysis of a flax (Linum usitatissimum L.) global collection

2020

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“…Molecular marker-based diversity is more precise and economic as it allows breeders to select unrelated individuals among thousands of genotypes within a short period of time which in turn reduces eld workload by evaluating only unrelated genotypes. Different molecular marker techniques such as RAPD, AFLP, ISSR, SSR and IRAP has been used to assess the genetic diversity of ax germplasm (17)(18)(19)(20)(21)(22)(23). The availability of a ax reference genome (24) has created the opportunity of discovery and exploitation of SNP markers, which are abundant and well distributed throughout the genome.…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity analysis of a Flax (Linum usitatissimum L.) global collection

Hoque

Fiedler

Rahman

2020

Preprint

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Abstract Background A sustainable breeding program requires a minimum level of germplasm diversity to provide varied options for the selection of new breeding lines. To maximize genetic gain of the North Dakota State University (NDSU) flax breeding program, we aimed to increase the genetic diversity of its parental stocks by incorporating diverse genotypes. For this purpose, we analyzed the genetic diversity, linkage disequilibrium, and population sub-structure of 350 globally-distributed flax genotypes with 6,200 SNP markers Results All the genotypes tested clustered into seven sub-populations (P1 to P7) based on the admixture model and the output of neighbor-joining (NJ) tree analysis and principal coordinate analysis were in line with that of structure analysis. The largest sub-population separation arose from a cluster of NDSU/American genotypes with Turkish and Asian genotypes. All sub-populations showed moderate genetic diversity (average H = 0.22 and I = 0.34). The pairwise F st comparison revealed a great degree of divergence ( F st > 0.25) between most of the combinations. A whole collection mantel test showed significant positive correlation (r = 0.30 and p < 0.01) between genetic and geographic distances, whereas it was non-significant for all sub-populations except P4 and P5 (r= 0.251, 0.349 respectively and p < 0.05). In the entire collection, the mean linkage disequilibrium was 0.03 and it decayed to its half maximum within < 21 kb distance. Conclusions To maximize genetic gain, hybridization between NDSU stock (P5) and Asian individuals (P6) are potentially the best option as genetic differentiation between them is highest ( F st > 0.50). In contrast, low genetic differentiation between P5 and P2 may enhance the accumulation of favorable alleles for oil and fiber upon crossing to develop dual purpose varieties. As each sub-population consists of many genotypes, a Neighbor-Joining tree assists to identify distantly related genotypes. These results also inform genotyping decisions for future association mapping studies to ensure the identification of a sufficient number of molecular markers to tag all linkage blocks.

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“…In recent years, with the development of sequencing technology, development of high-quality molecular markers in the whole genome has been realised. Random ampli ed polymorphic DNA (RAPD) [3][4][5], ampli ed fragment length polymorphism (AFLP) [6,7], simple sequence repeats (SSR) [8][9][10][11][12][13][14], and single nucleotide polymorphism (SNP) [15][16][17][18][19][20][21] molecular markers have been identi ed in ax. However, there no research has been conducted on ax InDel molecular markers.…”

Section: Introductionmentioning

confidence: 99%

Development and application of novel InDel markers in flax (Linum usitatissimum L.) through whole-genome re-sequencing

Jiang

Pan

Liu

et al. 2022

Genet Resour Crop Evol

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Flax is an important oil and bre crop grown in Northern Europe, Canada, India, and China. The development of molecular markers has accelerated the process of ax 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 ax. However, the development of ax insertion/deletion (InDel) markers has not been reported. A total of 17,110 InDel markers were identi ed by comparing whole-genome re-sequencing data of two accessions (87 − 3 and 84 − 3) with the ax 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 ax chromosomes, while chromosome 10 (913) presented with the lowest number. From 17,110 InDel markers, 90 primers that were evenly distributed in the ax genome were selected. Thirty-two pairs of polymorphic primers were detected in two ax accessions, and the polymorphism rate was 40.70%. Furthermore, genetic diversity analysis, population structure and principal component analyse (PCA) divided 69 ax accessions into two categories, namely oilseed ax and bre ax 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 ax lipid biosynthesis and lipid metabolism. This study is the rst to develop InDel markers based on re-sequencing in ax and clustered the markers into two well-separated groups for oil and bre. The results demonstrated that InDel markers developed herein could be used for ax germplasm identi cation, genetic diversity analysis, and molecular marker-assisted breeding.

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Genetic diversity analysis using RAPD and ISSR markers revealed discrete genetic makeup in relation to fibre and oil content in Linum usitatissimum L. genotypes

Cited by 18 publications

References 26 publications

Genetic diversity analysis of a flax (Linum usitatissimum L.) global collection

Genetic diversity analysis of a flax (Linum usitatissimum L.) global collection

Genetic diversity analysis of a Flax (Linum usitatissimum L.) global collection

Development and application of novel InDel markers in flax (Linum usitatissimum L.) through whole-genome re-sequencing

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