Genetic characterization and association mapping in near-isogenic lines of waxy maize using seed characteristics and SSR markers

Kim, Hae-Ri; Jin, Kyu; Namgung, Min; Park, Ki Jin; Ryu, Si‐Hwan; Mo, Chang Yeun; Lee, Ju Kyong

doi:10.1007/s13258-020-01030-7

Cited by 18 publications

(15 citation statements)

References 44 publications

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“…A 23 bp insertion in exon 2 is important in waxy rice, resulting in the loss of GBSS function, which in turn causes the glutinous trait (Inukai et al, 2000 ; Wanchana et al, 2003 ; Teng et al, 2012 ). In parallel with waxy or glutinous rice, genetic identification and association mapping of the waxy gene in maize have been characterized in the recent decades (Huang et al, 2010 ; Hossain et al, 2019 ; Luo et al, 2020 ; Kim H. R. et al, 2021 ). The waxy gene of wild maize was located in chromosome 9 and comprised of 14 exons by 3.93 kb long (Luo et al, 2020 ), and has a higher genetic variation level than rice, representing most of the identified waxy mutations by insertions and deletions, such as wx-m9, wx-m5, wx-B3, wx-m1 , and wx-B4 (Huang et al, 2010 ).…”

Section: Discussionmentioning

confidence: 99%

“…These different origins of different amylose contents rice maybe because of different consumers' preference by regions, for example, low-amylose in Vietnam and some provinces of China, intermediate-amylose in Iran, Pakistan, Malaysia and the Philippines, and high-amylose in Myanmar and Sri Lanka, respectively (Calingacion et al, 2014 ). Like rice, in East Asia, mainly Korea and China, and Southeast Asian countries, glutinous maize production has been increasing due to a high consumption for its special waxy type (Sa et al, 2015 ) as well as the consumption pattern shifts from a traditional rice-based diet to a Western meat-based diet (Kim H. R. et al, 2021 ). Unlike the waxy locus of rice, maize has a higher genetic variation level within its waxy gene region (Huang et al, 2010 ).…”

Section: Introductionmentioning

confidence: 99%

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Haplotype Variations and Evolutionary Analysis of the Granule-Bound Starch Synthase I Gene in the Korean World Rice Collection

et al. 2021

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Granule-bound starch synthase I (GBSSI) is responsible for Waxy gene encoding the, which is involved in the amylose synthesis step of starch biosynthesis. We investigated the genotypic and haplotypic variations of GBSSI (Os06g0133000) gene, including its evolutionary relatedness in the nucleotide sequence level using single-nucleotide polymorphisms (SNPs), indels, and structural variations (SVs) from 475 Korean World Rice Collection (KRICE_CORE), which comprised 54 wild rice and 421 cultivated represented by 6 ecotypes (temperate japonica, indica, tropical japonica, aus, aromatic, and admixture) or in another way by 3 varietal types (landrace, weedy, and bred). The results revealed that 27 of 59 haplotypes indicated a total of 12 functional SNPs (fSNPs), identifying 9 novel fSNPs. According to the identified novel fSNPs, we classified the entire rice collection into three groups: cultivated, wild, and mixed (cultivated and wild) rice. Five novel fSNPs were localized in wild rice: four G/A fSNPs in exons 2, 9, and 12 and one T/C fSNP in exon 13. We also identified the three previously reported fSNPs, namely, a G/A fSNP (exon 4), an A/C fSNP (exon 6), and a C/T fSNP (exon 10), which were observed only in cultivated rice, whereas an A/G fSNP (exon 4) was observed exclusively in wild rice. All-against-all comparison of four varietal types or six ecotypes of cultivated rice with wild rice showed that the GBSSI diversity was higher only in wild rice (π = 0.0056). The diversity reduction in cultivated rice can be useful to encompass the origin of this gene GBSSI during its evolution. Significant deviations of positive (wild and indica under balancing selection) and negative (temperate and tropical japonica under purifying selection) Tajima's D values from a neutral model can be informative about the selective sweeps of GBSSI genome insights. Despite the estimation of the differences in population structure and principal component analysis (PCA) between wild and subdivided cultivated subgroups, an inbreeding effect was quantified by FST statistic, signifying the genetic relatedness of GBSSI. Our findings of a novel wild fSNPS can be applicable for future breeding of waxy rice varieties. Furthermore, the signatures of selective sweep can also be of informative into further deeper insights during domestication.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Haplotype Variations and Evolutionary Analysis of the Granule-Bound Starch Synthase I Gene in the Korean World Rice Collection

et al. 2021

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“…(2020) Association mapping SSR; SSR; SNP Maize ( Zea mays ); Chickpea; Maize ( Zea mays ) Jha et al. (2021) ; Kim et al. (2021a) ; López-Malvar et al.…”

Section: The Concept Of Molecular or Dna Markersmentioning

confidence: 99%

Basic concepts and methodologies of DNA marker systems in plant molecular breeding

Amiteye

2021

Heliyon

104

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The concepts, methodologies and applications of some of the major molecular or DNA markers commonly used in plant science have been presented. The general principles of molecular marker techniques have been elucidated with detailed explanation of some notable basic concepts associated with marker applications: marker polymorphism, dominant or co-dominant mode of inheritance, agronomic trait-marker linkage, genetic mutations and variation. The molecular marker methods that have been extensively reviewed are RFLP, RAPD, SCAR, AFLP, SSR, CpSSR, ISSR, RAMP, SAMPL, SRAP, SSCP, CAPS, SNP, DArT, EST, and STS. In addition, the practicality of the retrotransposon-based marker methods, IRAP, REMAP, RBIP, and IPBS, have been discussed. Moreover, some salient characteristics of DNA markers have been compared and the various marker systems classified as PCR-or non-PCR-based, dominantly or co-dominantly inherited, locus specific or non-specific as well as at the levels of marker polymorphism and efficiency of marker reproducibility. Furthermore, the principles and methods of the following DNA markers have been highlighted: Penta-primer amplification refractory mutation system (PARMS), Conserved DNA-Derived Polymorphism (CDDP), P450-based analogue (PBA) markers, Tubulin-Based Polymorphism (TBP), Inter-SINE amplified polymorphism (ISAP), Sequence specific amplified polymorphism (S-SAP), Intron length polymorphisms (ILPs), Inter small RNA polymorphism (iSNAP), Direct amplification of length polymorphisms (DALP), Promoter anchored amplified polymorphism (PAAP), Target region amplification polymorphism (TRAP), Conserved region amplification polymorphism (CoRAP), Start Codon Targeted (SCoT) Polymorphism, and Directed Amplification of Minisatellite DNA (DAMD). Some molecular marker applications that have been recently employed to achieve various objectives in plant research have also been outlined. This review will serve as a useful reference resource for plant breeders and other scientists, as well as technicians and students who require basic know-how in the use of molecular or DNA marker technologies.

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“…A breeding program to develop a new cultivar requires knowledge and understanding of the genetic diversity, genetic relationships, and population structure of the desired gene [29]. To identify the functional genetic properties of GBSSII gene and provide evolutionary insight, a deep sequencing analysis was performed for the whole genomes of the 475 Korean rice accessions (KRICE_CORE), and genetic variations were detected.…”

Section: Introductionmentioning

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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Genetic characterization and association mapping in near-isogenic lines of waxy maize using seed characteristics and SSR markers

Cited by 18 publications

References 44 publications

Haplotype Variations and Evolutionary Analysis of the Granule-Bound Starch Synthase I Gene in the Korean World Rice Collection

Haplotype Variations and Evolutionary Analysis of the Granule-Bound Starch Synthase I Gene in the Korean World Rice Collection

Basic concepts and methodologies of DNA marker systems in plant molecular breeding

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

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