Genetic dissection of starch paste viscosity characteristics in waxy maize revealed by high-density SNPs in a recombinant inbred line population

Hao, Dejun; Xue, Li; Yuan, Jing; Zhang, Zhenliang; Lu, Hailiang; Mao, Yuxiang; Shi, Mei; Huang, Xiaolan; Zhou, Guangfei

doi:10.1007/s11032-017-0652-6

Cited by 7 publications

(6 citation statements)

References 42 publications

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“…(Table 2). A similar range of r 2 explained by molecular markers was found in maize, in which 72 QTLs detected for seven RVA parameters accounted for 0.06 to 0.18 of the phenotypic variation by analyzing 198 families derived from a cross between two waxy maize parents [57]. In contrast, in biparental QTL mapping of cassava, [11] reported a large phenotypic variance explained by the qPT.1LG1 (0.48) for PastTemp and a range of 0.13 to 0.37 for PeakVisc, Hot-PVisc, Cold-PVisc, and SetBack.…”

Section: Plos Onesupporting

confidence: 57%

“…All told, six different genomic regions in high LD with the PeakVisc, Hot-PVisc, SetBack, Cold-PVisc, PastTemp, and FinalVis traits in cassava starch were identified. Similarly, in waxy maize, there are also reports of the presence of QTL clusters co-associated with two or more RVA parameters in conventional biparental QTL mapping [57]. In total, eight QTLs, for BreDow, PeakVisc, SetBack, FinalVis, SetBack, pasting time, and trough viscosity were co-located on chromosomes 2, 3, 4, 5, 7, and 9.…”

Section: Genome-wide Association Study For Cassava Starch Traitsmentioning

confidence: 91%

“…Other studies have reported that the genes GRMZM2G146028 (AP2/EREBP family transcription factor) on chromosome 4 and GRMZM2G142709 (glycosyltransferase) on chromosome 5 are likely candidate genes for QTLs qPV4-1 and qTV4-1, and qFV5-2, respectively, which regulate PeakVisc, trough viscosity, and FinalVis [57]. In other starchy species such as rice, a transcription factor of the AP2/EREBP family has been identified as a determinant in the physicochemical properties of starch, by regulating the starch biosynthesis underlying the amylopectin structure [75].…”

Section: Transcripts Most Likely Associated With Cassava Starch Paste Propertiesmentioning

confidence: 99%

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Genome-wide association study of cassava starch paste properties

Santos

Sousa²,

Brito³

et al. 2022

PLoS ONE

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An understanding of cassava starch paste properties (CSPP) can contribute to the selection of clones with differentiated starches. This study aimed to identify genomic regions associated with CSPP using different genome-wide association study (GWAS) methods (MLM, MLMM, and Farm-CPU). The GWAS was performed using 23,078 single-nucleotide polymorphisms (SNPs). The rapid viscoanalyzer (RVA) parameters were pasting temperature (PastTemp), peak viscosity (PeakVisc), hot-paste viscosity (Hot-PVisc), cool-paste viscosity (Cold-PVisc), final viscosity (FinalVis), breakdown (BreDow), and setback (Setback). Broad phenotypic and molecular diversity was identified based on the genomic kinship matrix. The broad-sense heritability estimates (h2) ranged from moderate to high magnitudes (0.66 to 0.76). The linkage disequilibrium (LD) declined to between 0.3 and 2.0 Mb (r2 <0.1) for most chromosomes, except chromosome 17, which exhibited an extensive LD. Thirteen SNPs were found to be significantly associated with CSPP, on chromosomes 3, 8, 17, and 18. Only the BreDow trait had no associated SNPs. The regional marker-trait associations on chromosome 18 indicate a LD block between 2907312 and 3567816 bp and that SNP S18_3081635 was associated with SetBack, FinalVis, and Cold-PVisc (all three GWAS methods) and with Hot-PVisc (MLM), indicating that this SNP can track these four traits simultaneously. The variance explained by the SNPs ranged from 0.13 to 0.18 for SetBack, FinalVis, and Cold-PVisc and from 0.06 to 0.09 for PeakVisc and Hot-PVisc. The results indicated additive effects of the genetic control of Cold-PVisc, FinalVis, Hot-PVisc, and SetBack, especially on the large LD block on chromosome 18. One transcript encoding the glycosyl hydrolase family 35 enzymes on chromosome 17 and one encoding the mannose-p-dolichol utilization defect 1 protein on chromosome 18 were the most likely candidate genes for the regulation of CSPP. These results underline the potential for the assisted selection of high-value starches to improve cassava root quality through breeding programs.

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Section: Plos Onesupporting

confidence: 57%

Section: Genome-wide Association Study For Cassava Starch Traitsmentioning

confidence: 91%

Section: Transcripts Most Likely Associated With Cassava Starch Paste Propertiesmentioning

confidence: 99%

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Genome-wide association study of cassava starch paste properties

Santos

Sousa²,

Brito³

et al. 2022

PLoS ONE

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“…Four maize lines were selected to extract starch, and the pasting properties of the starch were measured using a rapid visco analyser according to Hao et al . 51 .…”

Section: Methodsmentioning

confidence: 99%

Identification of Quantitative Trait Loci and Candidate Genes for Maize Starch Granule Size through Association Mapping

Liu

Zhang

Xue

et al. 2018

Sci Rep

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Starch is an important nutrient component of maize kernels, and starch granule size largely determines kernel waxiness, viscosity, and other physiochemical and processing properties. To explore the genetic basis of maize starch granule size, 266 tropical, subtropical, and temperate inbred lines were subjected to genome-wide association analyses with an array of 56,110 random single nucleotide polymorphisms (SNPs). In the present panel, the kernel starch granule size ranged from 7–15.8 µm long and 6.8–14.3 µm wide. Fourteen significant SNPs were identified as being associated with the length of starch granules and 9 with their width. One linkage disequilibrium block flanking both sides of a significant SNP was defined as a quantitative trait locus (QTL) interval, and seven QTLs were mapped for both granule length and width. A total of 79 and 88 candidate genes associated with starch length and width, respectively, were identified as being distributed on QTL genomic regions. Among these candidate genes, six with high scores were predicted to be associated with maize starch granule size. A candidate gene association analysis identified significant SNPs within genes GRMZM2G419655 and GRMZM2G511067, which could be used as functional markers in screening starch granule size for different commercial uses.

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“…Corn supplies rich nutrition the protein amino acid content of waxy corn kernels is between normal corn and high lysine corn (Zhao, Bai-Shan, Shi, Li, & Center, 2016), but the protein content is high (7% to 14.5%), and the germplasm content reaches 14.5% (Harakotr, Suriharn, Lertrat, & Scott, 2016;Seo, Park, Ryu, Park, & Choi, 2018). The edible quality traits of waxy corn are better than those of non-waxy corn, especially with respect to viscosity, sweetness and aroma (Hao et al, 2017;Zhao et al, 2016). The waxy corn taste is usually soft and delicate, sticky, thin and slag-free, with a slight amount of scent and sweetness, and waxy corn is easy to chew (Zhu, Li, & Shi, 2016).…”

Section: Introductionmentioning

confidence: 99%

Liquid chromatography combined with patter recognition to detect the metabolic profiling of corn kernels

Luo

et al. 2019

Food and Agricultural Immunology

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The aim of this study was to compare the components of waxy and non-waxy corn kernels from a metabolomic perspective. All samples were analysed by liquid chromatography-mass spectrometry (LC-MS) with mode+ and mode− to obtain spectral data. Unsupervised principal component analysis (PCA), Partial least squares discrimination analysis (PLS-DA) and orthogonal partial least squares discriminant analysis (OPLS-DA) were used to identify significant components of waxy and non-waxy corn kernels. A total of 1589 features in (ESI+) ion mode and 2310 features in (ESI-) ion mode were obtained in this project. OPLS-DA identified 117 differential metabolites, including citric acid, alphalinolenic metabolites, distinguished non-waxy corn from waxy corn. Compared with waxy corn, non-waxy corn expressed the enhanced metabolites such as guanine, guanosine and the reduced ones represented by citric acid, and oleic acid. This study offer new clues for the study of the taste and nutritional value of waxy and non-waxy corn.

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Genetic dissection of starch paste viscosity characteristics in waxy maize revealed by high-density SNPs in a recombinant inbred line population

Cited by 7 publications

References 42 publications

Genome-wide association study of cassava starch paste properties

Genome-wide association study of cassava starch paste properties

Identification of Quantitative Trait Loci and Candidate Genes for Maize Starch Granule Size through Association Mapping

Liquid chromatography combined with patter recognition to detect the metabolic profiling of corn kernels

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