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16 pages, 3539 KiB  
Article
The Wx/SSIIa and GS3/GW7 Alleles, Both Individually and in Combination, Can Significantly Distinguish Rice Germplasm Quality
by Yuanyuan Hao, Junfeng Xu, Mingming Wu, Ying Zhu, Jiayu Song, Yifei Han, Chunshou Li and Fudeng Huang
Int. J. Mol. Sci. 2025, 26(14), 6726; https://doi.org/10.3390/ijms26146726 - 14 Jul 2025
Viewed by 239
Abstract
As living standards rise, there has been a growing emphasis on quality traits related to rice’s taste potential. Recent studies explored correlations among quality traits, but the influence of major genes governing a specific quality trait on other quality traits remains elusive. Here, [...] Read more.
As living standards rise, there has been a growing emphasis on quality traits related to rice’s taste potential. Recent studies explored correlations among quality traits, but the influence of major genes governing a specific quality trait on other quality traits remains elusive. Here, we report on the application of grain quality genes, two of Waxy (Wx) and Starch synthase II-a (SSIIa), which dominates in rice cooking and eating quality, and two grain length/width-related genes, grain size 3 (GS3) and grain width 7 (GW7), on appearance quality traits. Five allele-specific markers for these genes were developed, and used to stack the desirable alleles at these loci. The effects of individual or combined alleles at the loci were evaluated using a set of 156 rice germplasm. We found that the Wx-In1 (Intron 1) locus exerts a major effect in controlling both amylose content and gel consistency, while the SSIIa-Ex8 (Exon 8) locus primarily governs alkali spreading value. The impact on chalkiness-related traits follows the hierarchy of Wx-In1 > SSIIa-Ex8 > Wx-Ex10 (Exon 10). GS3-Ex2 (Exon 2) has a highly significant impact on chalkiness-related traits, and the GW7-Pro (Promoter) locus exerts a synergistic effect. The GS3-Ex2 locus exerts an effect in controlling both gel consistency and alkali spreading value, while the GW7-Pro locus governs amylose content. The data for newly developed allele-specific markers will facilitate the improvement of rice quality in rice. Full article
(This article belongs to the Special Issue Molecular and Epigenetic Regulation in Seed Development)
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19 pages, 1111 KiB  
Article
Assessment of Rice Amylose Content and Grain Quality Through Marker-Assisted Selection
by Iris Pérez-Almeida, Oscar Navia-Pesantes and Roberto Celi-Herán
Int. J. Plant Biol. 2025, 16(2), 52; https://doi.org/10.3390/ijpb16020052 - 20 May 2025
Viewed by 1032
Abstract
Rice (Oryza sativa L.) is essential for global food security and sustains billions worldwide, emphasizing the need to improve production and quality. One key challenge in rice breeding is the inheritance and environmental sensitivity of amylose content, a starch component that influences [...] Read more.
Rice (Oryza sativa L.) is essential for global food security and sustains billions worldwide, emphasizing the need to improve production and quality. One key challenge in rice breeding is the inheritance and environmental sensitivity of amylose content, a starch component that influences the texture, water absorption, and firmness after cooking, which are crucial for market acceptance. While international markets prefer low-amylose varieties for their softness, intermediate- and high-amylose varieties are favored in Latin America for their firmness. The objective of this study was to develop a molecular quality assessment methodology that, combined with morphological and culinary evaluations, helps in the selection of rice varieties during the breeding process. First, ten Ecuadorian rice materials were evaluated for milling and culinary quality characteristics, revealing significant grain size, sterility, milling yield, cooking time, and texture variations. Amylose content (AC) is genetically regulated by the waxy gene and its allelic variants, affecting granule-bound starch synthase (GBSS) enzyme expression. Secondly, to classify rice varieties molecularly based on AC, the testing ten genotypes plus nine control varieties were analyzed using microsatellite (SSR) markers. The waxy molecular marker, combined with metaphor agarose gel electrophoresis (MAGE), proved effective for early-stage AC analysis, reducing variety selection costs and improving breeding efficiency. Additionally, a restriction enzyme protocol assay facilitated variety differentiation by selectively cleaving the waxy gene sequence at a specific single-nucleotide polymorphism (SNP) site, allowing for precise AC genetic classification. By integrating molecular techniques with traditional assessments, this study reveals that using marker-assisted selection in breeding programs, as well as supporting the identification and development of high-quality local rice varieties to meet market demands, improves production efficiency and optimizes the assessment of developing varieties under diverse environmental conditions. Full article
(This article belongs to the Section Plant Biochemistry and Genetics)
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18 pages, 2019 KiB  
Article
QTL Analysis of β-Glucan Content and Other Grain Traits in a Recombinant Population of Spring Barley
by Alberto Gianinetti, Roberta Ghizzoni, Francesca Desiderio, Caterina Morcia, Valeria Terzi and Marina Baronchelli
Int. J. Mol. Sci. 2024, 25(12), 6296; https://doi.org/10.3390/ijms25126296 - 7 Jun 2024
Cited by 1 | Viewed by 1390
Abstract
Barley with high grain β-glucan content is valuable for functional foods. The identification of loci for high β-glucan content is, thus, of great importance for barley breeding. Segregation mapping for the content in β-glucan and other barley grain components (starch, protein, lipid, ash, [...] Read more.
Barley with high grain β-glucan content is valuable for functional foods. The identification of loci for high β-glucan content is, thus, of great importance for barley breeding. Segregation mapping for the content in β-glucan and other barley grain components (starch, protein, lipid, ash, phosphorous, calcium, sodium) was performed using the progeny of the cross between Glacier AC38, a mutant with high amylose, and CDC Fibar, a high β-glucan waxy cultivar. The offspring of this cross showed transgressive segregation for β-glucan content. Linkage analysis based on single-nucleotide polymorphism (SNP) molecular markers was used for the genotyping of the parents and recombinant inbred lines (RILs). Two Quantitative Trait Loci (QTL) for β-glucan content and several QTL for other grain components were found. The former ones, located on chromosomes 1H and 7H, explained 27.9% and 27.4% of the phenotypic variance, respectively. Glacier AC38 provided the allele for high β-glucan content at the QTL on chromosome 1H, whereas CDC Fibar contributed the allele at the QTL on chromosome 7H. Their recombination resulted in a novel haplotype with higher β-glucan content, up to 18.4%. Candidate genes are proposed for these two QTL: HvCslF9, involved in β-glucan biosynthesis, for the QTL on chromosome 1H; Horvu_PLANET_7H01G069300, a gene encoding an ATP-Binding Cassette (ABC) transporter, for the QTL on chromosome 7H. Full article
(This article belongs to the Special Issue Molecular Genetics and Plant Breeding 4.0)
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12 pages, 1160 KiB  
Article
Deciphering the Role of Waxy Gene Mutations in Enhancing Rice Grain Quality
by Yong Yang, Lihui Zhou, Linhao Feng, Jianying Jiang, Lichun Huang, Qing Liu, Yadong Zhang, Changquan Zhang and Qiaoquan Liu
Foods 2024, 13(11), 1624; https://doi.org/10.3390/foods13111624 - 23 May 2024
Cited by 3 | Viewed by 1738
Abstract
Amylose content (AC) stands as a pivotal determinant of rice grain quality, primarily governed by the Waxy gene (Wx). The allelic variation within this gene, particularly the presence of the Wxmp allele derived from the ancestral Wxmq allele, significantly [...] Read more.
Amylose content (AC) stands as a pivotal determinant of rice grain quality, primarily governed by the Waxy gene (Wx). The allelic variation within this gene, particularly the presence of the Wxmp allele derived from the ancestral Wxmq allele, significantly influences AC and is prevalent among soft japonica rice varieties in southern China. Although both alleles are associated with lower AC, there remains a paucity of detailed understanding regarding the interplay between specific functional single nucleotide polymorphisms (SNPs) within these alleles and the overarching rice grain quality. To investigate this, we engineered three distinct transgenic rice lines, each harboring the Wxmp, Wxmq, or Wxb−5c alleles in the background of the glutinous rice cultivar Nip(wx). This suite of transgenic rice lines showcased varying degrees of grain transparency inversely correlated to AC, which in turn influenced other physicochemical properties of the rice grains, such as taste value of cooked rice, gel consistency, and starch pasting properties. Additionally, analyses of gene expression and enzyme activity revealed that the functional SNPs, Ex4-53G to A and Ex5-53T to C, lead to a decline in the activity of granule-bound starch synthase I (GBSSI) without altering expression levels. Full article
(This article belongs to the Section Grain)
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19 pages, 6693 KiB  
Article
Population Structure and Genetic Diversity of Shanlan Landrace Rice for GWAS of Cooking and Eating Quality Traits
by Lin Zhang, Bowen Deng, Yi Peng, Yan Gao, Yaqi Hu and Jinsong Bao
Int. J. Mol. Sci. 2024, 25(6), 3469; https://doi.org/10.3390/ijms25063469 - 19 Mar 2024
Cited by 2 | Viewed by 2083
Abstract
The Shanlan landrace rice in Hainan Province, China, is a unique upland rice germplasm that holds significant value as a genetic resource for rice breeding. However, its genetic diversity and its usefulness in rice breeding have not been fully explored. In this study, [...] Read more.
The Shanlan landrace rice in Hainan Province, China, is a unique upland rice germplasm that holds significant value as a genetic resource for rice breeding. However, its genetic diversity and its usefulness in rice breeding have not been fully explored. In this study, a total of eighty-four Shanlan rice, three typical japonica rice cultivars, and three typical indica rice cultivars were subjected to resequencing of their genomes. As a result, 11.2 million high-quality single nucleotide polymorphisms (SNPs) and 1.6 million insertion/deletions (InDels) were detected. Population structure analysis showed all the rice accessions could be divided into three main groups, i.e., Geng/japonica 1 (GJ1), GJ2, and Xian/indica (XI). However, the GJ1 group only had seven accessions including three typical japonica cultivars, indicating that most Shanlan landrace rice are different from the modern japonica rice. Principal component analysis (PCA) showed that the first three principal components explained 60.7% of the genetic variation. Wide genetic diversity in starch physicochemical parameters, such as apparent amylose content (AAC), pasting viscosity, texture properties, thermal properties, and retrogradation representing the cooking and eating quality was also revealed among all accessions. The genome-wide association study (GWAS) for these traits was conducted and identified 32 marker trait associations in the entire population. Notably, the well-known gene Waxy (Wx) was identified for AAC, breakdown viscosity, and gumminess of the gel texture, and SSIIa was identified for percentage of retrogradation and peak gelatinization temperature. Upon further analysis of nucleotide diversity in Wx, six different alleles, wx, Wxa, Wxb, Wxin, Wxla/mw, and Wxlv in Shanlan landrace rice were identified, indicating rich gene resources in Shanlan rice for quality rice breeding. These findings are expected to contribute to the development of new rice with premium quality. Full article
(This article belongs to the Special Issue Molecular Research for Cereal Grain Quality 2.0)
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14 pages, 3630 KiB  
Article
The Breeding of Waxy Sorghum Using Traditional Three-Line Method and Marker-Assisted Selection
by Yong-Pei Wu, Yu-Chi Chang, Su-Chen Kuo, Dah-Jing Liao, Ting-Yu Shen, Hsin-I Kuo, Sheng-Wen Wang and Yu-Chien Tseng
Agriculture 2023, 13(11), 2054; https://doi.org/10.3390/agriculture13112054 - 26 Oct 2023
Cited by 2 | Viewed by 1908
Abstract
Sorghum (Sorghum bicolor) exhibits drought resistance and environmental adaptability, making it a crucial cereal crop for semi-arid regions. It has a wide range of uses, including as food, feed, brooms, alcohol production, and bioethanol. In particular, Taiwan imports nearly 50,000 tons [...] Read more.
Sorghum (Sorghum bicolor) exhibits drought resistance and environmental adaptability, making it a crucial cereal crop for semi-arid regions. It has a wide range of uses, including as food, feed, brooms, alcohol production, and bioethanol. In particular, Taiwan imports nearly 50,000 tons of sorghum annually, primarily for the production of sorghum liquor. However, the ideal raw material for high-quality sorghum liquor is waxy sorghum, and not all sorghum varieties imported or promoted in Taiwan are of this waxy type. Consequently, there is a shortage of sufficient waxy sorghum raw materials to meet the demands of the Taiwan market. The occurrence of waxy sorghum (wx) is caused by the mutation of granule-bound starch synthase I (GBBS I), and there are currently several known types of mutants, carrying different wxa, wxb, and wxc waxy alleles. Among them, wxc is a novel mutation type, and in native sorghum in Taiwan, individuals with the waxy allele wxc have been found. The three-line method is a commonly used breeding strategy, which simplifies the process of emasculation to obtain hybrid F1 offspring. In this study, imported sorghum variety Liangnuo No.1 (with male sterility), native glutinous sorghum variety SB6 from Taiwan (carrying the wxc waxy allele), and sorghum reference genome variety BTx623 were used as research materials. The goal was to use the three-line method to produce waxy sorghums, including the male sterile line (A-line), male sterile maintenance line (B-line), and fertility-restoring line (R-line). The breeding results showed that by using backcross breeding, molecular-assisted selection, and traditional field selection methods, high-quality three-line materials (A-, B-, R-lines, named CNA1, CNB1 CNR1, respectively) and F1 hybrid (CNH1) with favorable agronomic traits and yield quality were successfully obtained. Full article
(This article belongs to the Section Crop Genetics, Genomics and Breeding)
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19 pages, 2734 KiB  
Article
Main Characteristics of Processed Grain Starch Products and Physicochemical Features of the Starches from Maize (Zea mays L.) with Different Genotypes
by Eduard B. Khatefov, Vladimir G. Goldstein, Alexey V. Krivandin and Lyubov A. Wasserman
Polymers 2023, 15(8), 1976; https://doi.org/10.3390/polym15081976 - 21 Apr 2023
Cited by 1 | Viewed by 3861
Abstract
To understand the relationship between the genotype of maize plants and differences in their origin and the ploidy of the genome, which carry gene alleles programming the biosynthesis of various starch modifications, the thermodynamic and morphological features of starches from the grains of [...] Read more.
To understand the relationship between the genotype of maize plants and differences in their origin and the ploidy of the genome, which carry gene alleles programming the biosynthesis of various starch modifications, the thermodynamic and morphological features of starches from the grains of these plants have been studied. This study investigated the peculiarities of starch extracted from subspecies of maize (the dry matter mass (DM) fraction, starch content in grain DM, ash content in grain DM, and amylose content in starch) belonging to different genotypes within the framework of the program for the investigation of polymorphism of the world collection of plant genetic resources VIR. Among the starch genotypes of maize studied, four groups comprised the waxy (wx), conditionally high amylose (“ae”), sugar (su), and wild (WT) genotypes. Starches with an amylose content of over 30% conditionally belonged to the “ae” genotype. The starches of the su genotype had fewer starch granules than other investigated genotypes. An increase in amylose content in the investigated starches, accompanied by a decrease in their thermodynamic melting parameters, induced the accumulation of defective structures in the starches under study. The thermodynamic parameters evaluated for dissociation of the amylose–lipid complex were temperature (Taml) and enthalpy (Haml); for the su genotype, temperature and enthalpy values of dissociation of the amylose–lipid complex were higher than in the starches from the “ae” and WT genotypes. This study has shown that the amylose content in starch and the individual features of the maize genotype determine the thermodynamic melting parameters of the starches under study. Full article
(This article belongs to the Special Issue Biomass Polymers)
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19 pages, 3689 KiB  
Article
Three Starch Synthase IIa (SSIIa) Alleles Reveal the Effect of SSIIa on the Thermal and Rheological Properties, Viscoelasticity, and Eating Quality of Glutinous Rice
by Tsukine Nakano, Naoko Crofts, Satoko Miura, Naoko F. Oitome, Yuko Hosaka, Kyoko Ishikawa and Naoko Fujita
Int. J. Mol. Sci. 2023, 24(4), 3726; https://doi.org/10.3390/ijms24043726 - 13 Feb 2023
Cited by 6 | Viewed by 2223
Abstract
Glutinous rice accumulates amylose-free starch and is utilized for rice cakes and crackers, owing to the loss of the Waxy gene which encodes granule-bound starch synthase I (GBSSI). Starch synthase IIa (SSIIa) elongates amylopectin chains with a degree of polymerization (DP) of 6–12 [...] Read more.
Glutinous rice accumulates amylose-free starch and is utilized for rice cakes and crackers, owing to the loss of the Waxy gene which encodes granule-bound starch synthase I (GBSSI). Starch synthase IIa (SSIIa) elongates amylopectin chains with a degree of polymerization (DP) of 6–12 to 13–24 and greatly influences starch properties. To elucidate the relationship between the branch length of amylopectin and the thermal and rheological properties, viscoelasticity, and eating quality of glutinous rice, three allelic near isogenic lines with high, low, or no SSIIa activity were generated (designated as SS2a wx, ss2aL wx, and ss2a wx, respectively). Chain length distribution analyses revealed that ss2a wx exhibited the highest short chain (DP < 12) number and lowest gelatinization temperature, whereas SS2a wx showed the opposite results. Gel filtration chromatography showed that the three lines contained essentially no amylose. Viscoelasticity analyses of rice cakes stored at low temperature for different durations revealed that ss2a wx maintained softness and elasticity for up to 6 days, while SS2a wx hardened within 6 h. Sensory evaluation was consistent with mechanical evaluation. The relationship of amylopectin structure with the thermal and rheological properties, viscoelasticity, and eating quality of glutinous rice is discussed. Full article
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11 pages, 4769 KiB  
Article
Genome-Wide Association Study (GWAS) Reveals an SNP Associated with Waxy Trait and Development of a Functional Marker for Predicting Waxy Maize (Zea mays L. var. ceratina)
by Vinitchan Ruanjaichon, Khin Kyawt Yin, Burin Thunnom, Kanogporn Khammona, Khundej Suriharn, Sakunkan Simla, Chalong Kerdsri, Wanchana Aesomnuk, Arweewut Yongsuwan, Naraporn Chaomueang, Nay Nay Oo, Jintana Unartngam, Siwaret Arikit, Samart Wanchana and Theerayut Toojinda
Agronomy 2022, 12(10), 2289; https://doi.org/10.3390/agronomy12102289 - 23 Sep 2022
Cited by 3 | Viewed by 3802
Abstract
Waxy maize (Zea mays L. var. ceratina) is a special type of maize characterized by a sticky texture when cooked, due to high amylopectin content in the endosperm. Waxy maize is popular in China and Southeast Asia for fresh consumption. Breeding strategies [...] Read more.
Waxy maize (Zea mays L. var. ceratina) is a special type of maize characterized by a sticky texture when cooked, due to high amylopectin content in the endosperm. Waxy maize is popular in China and Southeast Asia for fresh consumption. Breeding strategies have been used to improve the quality of waxy maize, including hybrid breeding by crossing super sweet maize and waxy maize. However, the lack of a marker has limited the efficiency of breeding for the waxy trait, especially because the waxy allele is recessive. In this study, we conducted a genome-wide association study (GWAS) in an association panel consisting of 213 inbred lines and recombinant inbred lines (RILs) of field maize and waxy maize to identify loci associated with the waxy kernel phenotype. The genotypic data were 155,768 SNPs derived from the high-density 600 K maize genotyping array for single-nucleotide polymorphisms (SNPs). The GWAS results identified the qWx9 locus on chromosome 9 (25.06–25.18 Mb) associated with the trait. Based on the most significantly associated SNP (AX-90613979, −log10(P) = 6.8)), which was located on Wx1, a MassArray marker was developed and validated in a panel of 139 maize lines containing waxy maize and sweet maize with different amylose content. The newly developed marker had a significant association with amylose content (R2 value of 0.81, p < 0.001) and clearly distinguished between waxy maize and sweet maize lines that had different amylose content. This marker will be useful for maize breeding programs for the waxy trait, as well as for breeding programs for hybrid maize combining the sweetness and waxy traits. The gene-based SNP markers could aid breeders by eliminating the costs and time required to perform lengthy field trials and help to accelerate sweet maize and waxy maize breeding programs. Full article
(This article belongs to the Topic Plant Breeding, Genetics and Genomics)
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14 pages, 2122 KiB  
Article
Combined Effects of Different Alleles of FLO2, Wx and SSIIa on the Cooking and Eating Quality of Rice
by Yu Zhang, Jiajia Zhao, Yaqi Hu, Yanni Zhang, Yining Ying, Feifei Xu and Jinsong Bao
Plants 2022, 11(17), 2249; https://doi.org/10.3390/plants11172249 - 30 Aug 2022
Cited by 7 | Viewed by 2191
Abstract
The improvement of the cooking and eating quality (CEQ) of rice is one of the major objectives of current rice-breeding programs. A few major genes such as Waxy (Wx) and starch synthase IIa (SSIIa) have been successfully applied in [...] Read more.
The improvement of the cooking and eating quality (CEQ) of rice is one of the major objectives of current rice-breeding programs. A few major genes such as Waxy (Wx) and starch synthase IIa (SSIIa) have been successfully applied in molecular breeding. However, their interactive effects on CEQ have not been fully understood. In this study, a recombinant inbred line (RIL) population was constructed by crossing the white-core mutant GM645 with the transparent phenotype of the japonica rice variety Tainung 67 (TN67). GM645 and TN67 contain different alleles of FLOURY ENDOSPERM2 (FLO2), Wx, and SSIIa. The effects of different allele combinations of FLO2, Wx, and SSIIa on the CEQ of rice were investigated. The inbred lines with the mutation allele flo2 had a significantly lower apparent amylose content (AAC), viscosity characteristics except for setback (SB), and gel texture properties compared to those lines with the FLO2 allele. The allelic combination of FLO2 and Wx significantly affected the AAC, breakdown (BD), and gel textural properties, which could explain most of the variations in those rice quality traits that were correlated with AAC. The allelic combination of FLO2 and SSIIa significantly affected the hot paste viscosity (HPV) and pasting temperature (PT). The Wx × SSIIa interaction had a significant effect on the PT. The interaction of FLO2, Wx and SSIIa significantly affected the AAC, cold paste viscosity (CPV), PT, and consistency viscosity (CS). These results highlight the important roles of these quality-related genes in regulating the CEQ of rice and provide new clues for rice-quality improvement by marker-assisted selection. Full article
(This article belongs to the Special Issue Germplasm Enhancement and Breeding for Rice Quality Improvement)
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14 pages, 1775 KiB  
Article
Development of the PARMS Markers of the Waxy Gene and Utilization in Discriminating Wild Accessions, and Cultivated Rice (Oryza sativa L.) with Different Eating and Cooking Quality
by Guibeline Charlie Jeazet Dongho Epse Mackon, Enerand Mackon, Yafei Ma, Yitong Zhao, Yuhang Yao, Xianggui Dai and Piqing Liu
Agronomy 2022, 12(6), 1294; https://doi.org/10.3390/agronomy12061294 - 28 May 2022
Cited by 7 | Viewed by 3191
Abstract
Amylose content (AC) is the major indicator of rice eating and cooking quality (ECQ). Its synthesis in rice endosperm is mainly regulated by the protein, granule-bound starch synthase 1, which is encoded by the waxy gene (Os06g0133000, LOC_Os06g04200). The diversity of AC is [...] Read more.
Amylose content (AC) is the major indicator of rice eating and cooking quality (ECQ). Its synthesis in rice endosperm is mainly regulated by the protein, granule-bound starch synthase 1, which is encoded by the waxy gene (Os06g0133000, LOC_Os06g04200). The diversity of AC is largely attributable to the allelic variation at the Wx locus and the development of effective and accurate functional molecular markers to target rice variant alleles is crucial in the breeding strategy. In the present study, we developed six pairs of penta-primer amplification refractory mutation system (PARMS) markers to distinguish between Wxlv, Wxa, Wxin, Wxb, Wxmp, and Wxop,hp. These markers were successfully used to screen the genotype of large assets of genetic resources including 98 wild accessions, 55 cultivars, and 22 parental lines. Our results showed that Wxb in a low AC type was predominant in Guangxi cultivated rice as a result of cultural preference, while Wxlv in the wild accessions. Moreover, our findings surprisingly revealed the presence of Wxb in wild accession, which is a new outcome that may contribute to understanding the origin, selection and domestication processes of rice. These functional markers could be effectively used in marker-assisted breeding to improve selection efficiency of cultivars with desired AC in the early generation. Full article
(This article belongs to the Special Issue Marker Development in the Genomics Era)
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15 pages, 4380 KiB  
Article
Allelic Diversification of the Wx and ALK Loci in Indica Restorer Lines and Their Utilisation in Hybrid Rice Breeding in China over the Last 50 Years
by Li-Xu Pan, Zhi-Zhong Sun, Chang-Quan Zhang, Bu Li, Qing-Qing Yang, Fei Chen, Xiao-Lei Fan, Dong-Sheng Zhao, Qi-Ming Lv, Ding-Yang Yuan and Qiao-Quan Liu
Int. J. Mol. Sci. 2022, 23(11), 5941; https://doi.org/10.3390/ijms23115941 - 25 May 2022
Cited by 5 | Viewed by 2310
Abstract
Hybrid rice technology has been used for more than 50 years, and eating and cooking quality (ECQ) has been a major focus throughout this period. Waxy (Wx) and alkaline denaturation (ALK) genes have received attention owing to their pivotal [...] Read more.
Hybrid rice technology has been used for more than 50 years, and eating and cooking quality (ECQ) has been a major focus throughout this period. Waxy (Wx) and alkaline denaturation (ALK) genes have received attention owing to their pivotal roles in determining rice characteristics. However, despite significant effort, the ECQ of restorer lines (RLs) has changed very little. By contrast, obvious changes have been seen in inbred rice varieties (IRVs), and the ECQ of IRVs is influenced by Wx, which reduces the proportion of Wxa and increases the proportion of Wxb, leading to a decrease in amylose content (AC) and an increase in ECQ. Meanwhile, ALK is not selected in the same way. We investigated Wx alleles and AC values of sterile lines of female parents with the main mating combinations in widely used areas. The results show that almost all sterile lines were Wxa-type with a high AC, which may explain the low ECQ of hybrid rice. Analysis of hybrid rice varieties and RLs in the last 5 years revealed serious homogenisation among hybrid rice varieties. Full article
(This article belongs to the Special Issue Molecular Research for Cereal Grain Quality)
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10 pages, 1752 KiB  
Article
Genetic Analysis of a Collection of Rice Germplasm (Oryza sativa L.) through High-Density SNP Array Provides Useful Information for Further Breeding Practices
by Ping Huang, Qiongyao Gu, Yong Hu, Huahui Li, Zhigang Wu, Weihua Liu, Zhenhua Zhu, Pingrong Yuan, Liu Duan, Ying Zhou, Hanyu Luo, Shuyan Kou and Li Liu
Genes 2022, 13(5), 830; https://doi.org/10.3390/genes13050830 - 6 May 2022
Cited by 11 | Viewed by 2738
Abstract
Traditional breeding strategies mainly focus on the evaluation of trait performance, but pay less attention to the changing genetic background. A comprehensive understanding of the genetic diversity of germplasms is crucial for the deliberate improvement of specific traits. A collection of 154 highland [...] Read more.
Traditional breeding strategies mainly focus on the evaluation of trait performance, but pay less attention to the changing genetic background. A comprehensive understanding of the genetic diversity of germplasms is crucial for the deliberate improvement of specific traits. A collection of 154 highland rice varieties were collected as the initial genetic resource in our breeding program to improve the pathogen resistance and eating and cooking qualities. These varieties were analyzed using a whole-genome SNP array and were clustered into three groups. Further analysis revealed that the favorable alleles of pathogen resistance genes are mostly absent in our collected varieties. However, it showed that most varieties possess favorable alleles of Waxy (Wx) and ALKALI DEGENERATION (ALK), which are able to enhance the eating and cooking qualities. Moreover, only about one fifth of all varieties harbors favorable the allele of fragrance gene Betainealdehyde dehydrogenase (BADH2). Together, these results give an overall view of the genetic constitution of the target traits, which provide useful information for future genetic improvement in breeding practices. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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12 pages, 1779 KiB  
Article
The Physicochemical Properties of Starch Are Affected by Wxlv in Indica Rice
by Linhao Feng, Chenya Lu, Yong Yang, Yan Lu, Qianfeng Li, Lichun Huang, Xiaolei Fan, Qiaoquan Liu and Changquan Zhang
Foods 2021, 10(12), 3089; https://doi.org/10.3390/foods10123089 - 13 Dec 2021
Cited by 8 | Viewed by 3208
Abstract
Amylose largely determines rice grain quality profiles. The process of rice amylose biosynthesis is mainly driven by the waxy (Wx) gene, which also affects the diversity of amylose content. The present study assessed the grain quality profiles, starch fine structure, and [...] Read more.
Amylose largely determines rice grain quality profiles. The process of rice amylose biosynthesis is mainly driven by the waxy (Wx) gene, which also affects the diversity of amylose content. The present study assessed the grain quality profiles, starch fine structure, and crystallinity characteristics of the near-isogenic lines Q11(Wxlv), NIL(Wxa), and NIL(Wxb) in the indica rice Q11 background containing different Wx alleles. Q11(Wxlv) rice contained a relatively higher amylose level but very soft gel consistency and low starch viscosity, compared with rice lines carrying Wxa and Wxb. In addition, starch fine structure analysis revealed a remarkable decrease in the relative area ratio of the short amylopectin fraction but an increased amylose fraction in Q11(Wxlv) rice. Chain length distribution analysis showed that Q11(Wxlv) rice contained less amylopectin short chains but more intermediate chains, which decreased the crystallinity and lamellar peak intensity, compared with those of NIL(Wxa) and NIL(Wxb) rice. Additionally, the starches in developing grains showed different accumulation profiles among the three rice lines. Moreover, significant differences in starch gelatinization and retrogradation characteristics were observed between near-isogenic lines, which were caused by variation in starch fine structure. These findings revealed the effects of Wxlv on rice grain quality and the fine structure of starch in indica rice. Full article
(This article belongs to the Section Grain)
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10 pages, 1859 KiB  
Article
Fast and Inexpensive Phenotyping and Genotyping Methods for Evaluation of Barley Mutant Population
by Yudai Kawamoto, Hirotaka Toda, Hiroshi Inoue, Kappei Kobayashi, Naoto Yamaoka, Takuya Araki and Takashi Yaeno
Plants 2020, 9(9), 1153; https://doi.org/10.3390/plants9091153 - 6 Sep 2020
Cited by 3 | Viewed by 3490
Abstract
To further develop barley breeding and genetics, more information on gene functions based on the analysis of the mutants of each gene is needed. However, the mutant resources are not as well developed as the model plants, such as Arabidopsis and rice. Although [...] Read more.
To further develop barley breeding and genetics, more information on gene functions based on the analysis of the mutants of each gene is needed. However, the mutant resources are not as well developed as the model plants, such as Arabidopsis and rice. Although genome editing techniques have been able to generate mutants, it is not yet an effective method as it can only be used to transform a limited number of cultivars. Here, we developed a mutant population using ‘Mannenboshi’, which produces good quality grains with high yields but is susceptible to disease, to establish a Targeting Induced Local Lesions IN Genomes (TILLING) system that can isolate mutants in a high-throughput manner. To evaluate the availability of the prepared 8043 M3 lines, we investigated the frequency of mutant occurrence using a rapid, visually detectable waxy phenotype as an indicator. Four mutants were isolated and single nucleotide polymorphisms (SNPs) were identified in the Waxy gene as novel alleles. It was confirmed that the mutations could be easily detected using the mismatch endonuclease CELI, revealing that a sufficient number of mutants could be rapidly isolated from our TILLING population. Full article
(This article belongs to the Special Issue Plant Mutation Breeding)
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