Genetic Diversity Analysis of Korean Peanut Germplasm Using 48 K SNPs ‘Axiom_Arachis’ Array and Its Application for Cultivar Differentiation

Nabi, Rizwana Begum Syed; Cho, Kwang-Soo; Tayade, Rupesh; Oh, Ki Won; Lee, Myoung Hee; Kim, Jung In; Kim, Sung-Up; Pae, Suk-Bok; Oh, Eunyoung

doi:10.21203/rs.3.rs-154213/v1

Cited by 3 publications

(3 citation statements)

References 49 publications

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“…Based on 3,474 SNPs, the genetic diversity of these 31 accessions was investigated using several approaches. As a whole, this panel has an average PIC, expected He, MAF and genetic distance of 0.16, 0.19, 0.86, 0.17, respectively, which is concordant with previous research using SNP genotyping 39,40,41 . In terms of the marker polymorphism, the PIC value is an indicator of markers that can reveal polymorphisms.…”

Section: Discussionsupporting

confidence: 90%

“…The average PIC of 0.16 from these 31 accessions falls in this last class, while 32% of the identified SNPs correspond to the reasonably informative class. In studies of other germplasm collections, the mean PIC value ranged from 0.08 to 0.26 even though some of these collections had a mixture of four market-type accessions including the U.S. Peanut mini core collection 39,40,41 , implying that the germplasm panel of 31 accessions chosen in this study preserves a high proportion of overall genetic diversity in spite of a smaller sample size. Concerning the origin of our germplasm, the global subset (n = 17) has a higher average PIC value (0.15) than the local subset (0.13 with n = 14).…”

Section: Discussionmentioning

confidence: 86%

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Assessment of genetic diversity and SNP marker development within peanut germplasm in Taiwan by RAD-seq

Hsu

Wang²,

Tseng

et al. 2022

Preprint

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The cultivated peanut (Arachis hypogaea L.) is an important oil crop but has a narrow genetic diversity. Molecular markers can be used to probe the genetic diversity of various germplasm. In this study, the restriction site associated DNA (RAD) approach was utilized to sequence 31 accessions of Taiwanese peanut germplasm, leading to the identification of a total of 17,610 single nucleotide polymorphisms (SNPs). The origin of these 31 accessions is contrasted so the global subset (n = 17) has greater genetic diversity than the local subset (n = 14). Concerning botanical varieties, the var. fastigiata subset has greater genetic diversity than the other two subsets of var. vulgaris and var. hypogaea, suggesting that novel genetic resources should be introduced into breeding programs to enhance genetic diversity. Principal component analysis (PCA) using genotyping data separated the 31 accessions into three clusters largely according to the botanical varieties, consistent with the PCA result for 282 accessions genotyped by 14 kompetitive allele-specific PCR (KASP) markers developed in this study. The SNP markers identified in this work not only revealed the genetic relationship and population structure of current germplasm in Taiwan, but also offer an efficient tool for breeding and further genetic applications.

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Section: Discussionsupporting

confidence: 90%

Section: Discussionmentioning

confidence: 86%

Assessment of genetic diversity and SNP marker development within peanut germplasm in Taiwan by RAD-seq

Hsu

Wang²,

Tseng

et al. 2022

Preprint

View full text Add to dashboard Cite

show abstract

“…The availability of the completed genome sequencing of peanuts provided ideal resource for genome-wide identi cation of SSR and SNP markers in silico (Zhao et al, 2017. In addition, large-scale 58K SNP Array (Axiom_Arachis, v1) and 48K SNP Array (Axiom_Arachis2, v2) have been developed, which provide a new chance for genetic analysis, constructing high-resolution linkage maps, and QTL mapping (Clevenger et al, 2017, Clevenger et al, 2018b, Nabi et al, 2021. Moreover, great efforts have been made in the genetic map construction, ne mapping, and MAS of peanut (Agarwal et al, 2018, Han et al, 2018.…”

Section: Introductionmentioning

confidence: 99%

BSA‑seq and genetic mapping reveals AhRt2 as a candidate gene responsible for red testa of peanut

Zhang

Yüan²,

Xia

et al. 2022

Theor Appl Genet

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Testa color is an important trait of peanut (Arachis hypogaea L.). Peanuts with red testa are rich in anthocyanin, are very popular with consumers. However, genes responsible for the red testa trait in peanut are rarely reported. In order to ne map red testa gene, two F 4 populations were constructed through the cross of YZ9102 (pink testa) with ZH12 (red testa) and Zhanhong2 (red testa). Genetic analysis indicated that red testa was controlled by a single recessive gene, and named as AhRt2 (Red testa gene 2). Using BSA-seq approach, AhRt2 was preliminary identi ed in chromosome 12, and further mapped to a 530-kb interval using 220 recombinant lines through linkage mapping. Functional annotation, expression pro ling, and sequence variation analyses con rmed that the anthocyanin reductase (ANR), Arahy.IK60LM, was the most likely candidate gene for AhRt2. A SNP in the third exon of AhRt2 changed the encoding amino acids, was associated with red testa of peanut. In addition, a closely linkaged molecular marker to red testa trait was developed. Our result provide insight into the molecular mechanism underlying peanut testa color and provide valuable diagnostic marker for marker-assisted selected (MAS) breeding in peanut. Key MessageThe candidate recessive gene AhRt2 responsible for red testa of peanut was identi ed thorugh combined BSA-seq and linkage mapping approaches.

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BSA‑Seq and Genetic Mapping Reveals AhRt2 as a Candidate Gene Responsible for Red Testa of Peanut

Zhang

Yüan

Xia

et al. 2021

Preprint

View full text Add to dashboard Cite

Testa color is an important trait of peanut (Arachis hypogaea L.). Peanuts with red testa are rich in anthocyanin, are very popular with consumers. However, genes responsible for the red testa trait in peanut are rarely reported. In order to fine map red testa gene, two F4 populations were constructed through the cross of YZ9102 (pink testa) with ZH12 (red testa) and Zhanhong2 (red testa). Genetic analysis indicated that red testa was controlled by a single recessive gene, and named as AhRt2 (Red testa gene 2). Using BSA-seq approach, AhRt2 was preliminary identified in chromosome 12, and further mapped to a 530-kb interval using 220 recombinant lines through linkage mapping. Functional annotation, expression profiling, and sequence variation analyses confirmed that the anthocyanin reductase (ANR), Arahy.IK60LM, was the most likely candidate gene for AhRt2. A SNP in the third exon of AhRt2 changed the encoding amino acids, was associated with red testa of peanut. In addition, a closely linkaged molecular marker to red testa trait was developed. Our result provide insight into the molecular mechanism underlying peanut testa color and provide valuable diagnostic marker for marker-assisted selected (MAS) breeding in peanut.

show abstract

Genetic Diversity Analysis of Korean Peanut Germplasm Using 48 K SNPs ‘Axiom_Arachis’ Array and Its Application for Cultivar Differentiation

Cited by 3 publications

References 49 publications

Assessment of genetic diversity and SNP marker development within peanut germplasm in Taiwan by RAD-seq

Assessment of genetic diversity and SNP marker development within peanut germplasm in Taiwan by RAD-seq

BSA‑seq and genetic mapping reveals AhRt2 as a candidate gene responsible for red testa of peanut

BSA‑Seq and Genetic Mapping Reveals AhRt2 as a Candidate Gene Responsible for Red Testa of Peanut

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