Development of intron length polymorphic (ILP) markers in onion (Allium cepa L.), and their cross-species transferability in garlic (A. sativum L.) and wild relatives

Jayaswall, Kuldip; Sharma, Himanshu; Bhandawat, Abhishek; Sagar, R.; Yadav, Vinod Kumar; Sharma, Vikas; Mahajan, Vijay; Roy, Joy; Singh, Major

doi:10.1007/s10722-019-00808-3

Cited by 32 publications

(19 citation statements)

References 23 publications

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“…Genetic variations (alleles) in crop species, such as SNPs, InDels, and intron length polymorphisms (ILPs), are essential to revealing molecular mechanisms, as they function in controlling traits [47][48][49][50]. Genetic variations of the starch synthase gene family has recently been updated in rice giving new insights into their correlation with improved amylose content and eating quality [20].…”

Section: Discussionmentioning

confidence: 99%

Functional Haplotypes and Evolutionary Insight into the Granule-Bound Starch Synthase II (GBSSII) Gene in Korean Rice Accessions (KRICE_CORE)

Maung

Chu

Park

2021

Foods

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Granule-bound starch synthase 2 (GBSSII), a paralogous isoform of GBSSI, carries out amylose biosynthesis in rice. Unlike GBSSI, it mainly functions in transient organs, such as leaves. Despite many reports on the starch gene family, little is known about the genetics and genomics of GBSSII. Haplotype analysis was conducted to unveil genetic variations (SNPs and InDels) of GBSSII (OS07G0412100) and it was also performed to gain evolutionary insight through genetic diversity, population genetic structure, and phylogenetic analyses using the KRICE_CORE set (475 rice accessions). Thirty nonsynonymous SNPs (nsSNPs) were detected across the diverse GBSSII coding regions, representing 38 haplotypes, including 13 cultivated, 21 wild, and 4 mixed (a combination of cultivated and wild) varieties. The cultivated haplotypes (C_1–C_13) contained more nsSNPs across the GBSSII genomic region than the wild varieties. Nucleotide diversity analysis highlighted the higher diversity values of the cultivated varieties (weedy = 0.0102, landrace = 0.0093, and bred = 0.0066) than the wild group (0.0045). The cultivated varieties exhibited no reduction in diversity during domestication. Diversity reduction in the japonica and the wild groups was evidenced by the negative Tajima’s D values under purifying selection, suggesting the domestication signatures of GBSSII; however, balancing selection was indicated by positive Tajima’s D values in indica. Principal component analysis and population genetics analyses estimated the ambiguous evolutionary relationships among the cultivated and wild rice groups, indicating highly diverse structural features of the rice accessions within the GBSSII genomic region. FST analysis differentiated most of the classified populations in a range of greater FST values. Our findings provide evolutionary insights into GBSSII and, consequently, a molecular breeding program can be implemented for select desired traits using these diverse nonsynonymous (functional) alleles.

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Section: Discussionmentioning

confidence: 99%

Functional Haplotypes and Evolutionary Insight into the Granule-Bound Starch Synthase II (GBSSII) Gene in Korean Rice Accessions (KRICE_CORE)

Maung

Chu

Park

2021

Foods

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“…Analysis of the SSR and ILP genotyping data using MVSP software revealed genetic similarity that ranged from 91.7 to 46.7% within the 35 white onion genotypes (Table 3). Jayaswall et al (2019b) reported 0.04 (within A. cepa individuals) to 0.92 (between A. sativum and wild (Ac-Ag4ET) genetic distance among the selected species. Interestingly, current study In present study, the UPGMA dendrogram discriminated all the genotypes into two main clusters (cluster I and II) and two sub-clusters (IA and IB).…”

Section: Genetic Diversity Among White Onion Genotypesmentioning

confidence: 95%

“…All amplified bands were scored as presence (1) and absence (0) of a specific allele and an accession was assigned for a null allele, where an amplification product was not detected for a particular genotypemarker combination (Mahajan et al 2009;Jayaswall et al 2019b). Similar size fragments across all individuals produced by markers and the variable size fragments produced by individual marker were named were as monomorphic and polymorphic fragments, respectively.…”

Section: Molecular Data Analysismentioning

confidence: 99%

Identification and characterization of white onion (Allium cepa L.) genotypes for high total soluble solid content through molecular markers

Singh

Mahajan

Verma

et al. 2020

Genet Resour Crop Evol

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“…Although high throughput sequencing techniques are being developed nowadays, the use of variable markers present in candidate genes is still an interesting alternative for association studies. An approach known as intron length polymorphism (ILP), based on the alignment of EST cDNA sequences against known genomic sequences, has been applied to a range of crop species for genetic diversity, evolutionary and association genetic studies [ 15 , 16 , 17 , 18 , 19 , 20 , 21 ]. As ILP markers are gene-based, co-dominant, neutral, convenient, reliable and cost effective, and can play a vital role in regulation of gene expression [ 22 ], this is a promising approach to genetic studies such as candidate gene association mapping, which seeks to identify allelic variation in the genes that influence girth growth.…”

Section: Introductionmentioning

confidence: 99%

Identification of Candidate Gene-Based Markers for Girth Growth in Rubber Trees

Bhusudsawang

Rattanawong²,

Phumichai³

et al. 2021

Plants

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Girth growth is an important factor in both latex and timber production of the rubber tree. In this study, we performed candidate gene association mapping for girth growth in rubber trees using intron length polymorphism markers (ILP) in identifying the candidate genes responsible for girth growth. The COBL064_1 marker developed from the candidate gene (COBL4) regulating cellulose deposition and oriented cell expansion in the plant cell wall showed the strongest association with girth growth across two seasons in the Amazonian population and was validated in the breeding lines. We then applied single molecule real-time (SMRT) circular consensus sequencing (CCS) to analyze a wider gene region of the COBL4 to pinpoint the single nucleotide polymorphism (SNP) that best explains the association with the traits. A SNP in the 3’ UTR showing linkage disequilibrium with the COBL064_1 most associated with girth growth. This study showed that the cost-effective method of ILP gene-based markers can assist in identification of SNPs in the candidate gene associated with girth growth. The SNP markers identified in this study added useful markers for the improvement of girth growth in rubber tree breeding programs.

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Development of intron length polymorphic (ILP) markers in onion (Allium cepa L.), and their cross-species transferability in garlic (A. sativum L.) and wild relatives

Cited by 32 publications

References 23 publications

Functional Haplotypes and Evolutionary Insight into the Granule-Bound Starch Synthase II (GBSSII) Gene in Korean Rice Accessions (KRICE_CORE)

Functional Haplotypes and Evolutionary Insight into the Granule-Bound Starch Synthase II (GBSSII) Gene in Korean Rice Accessions (KRICE_CORE)

Identification and characterization of white onion (Allium cepa L.) genotypes for high total soluble solid content through molecular markers

Identification of Candidate Gene-Based Markers for Girth Growth in Rubber Trees

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