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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: 10 May 2025 | Viewed by 11200

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Prof. Dr. Jinsong Bao

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Guest Editor

College of Agricultural and Biotechnology, Zhejiang University, Hangzhou 310058, China
Interests: rice grain quality
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue is the second volume of our previous Special Issue "Molecular Research for Cereal Grain Quality".

While cereal production is important for food security, cereal grain quality features determine consumer acceptability and market value. With the increase in standard of living, our desire for a better life requires more production of high-quality cereal foods. However, our ability to provide high-quality cereal grains is constrained due to a limited understanding of the molecular mechanisms of grain quality formation. Starch, proteins, and lipids are major compositions in all the cereals, while some compositions are present in a unique cereal. The biosynthesis and regulation mechanisms on the accumulation of these major or minor compositions in the cereal grain affect the end-use quality of cereals. Structure–function relations are important clues necessary for understanding which factors affect the grain quality. However, more molecular studies are necessary to discover the regulation mechanism underlying grain quality formation for the improvement of grain quality. This Special Issue aims to provide a forum on the most recent advances in the field of application of molecular tools to understand the mechanisms used for improving the grain quality in any cereals.

Any papers using novel molecular tools to solve problems in cereal grain quality are welcome. The molecular tools include (but are not limited to) genetic mapping, transformation, genome editing, genome selection, omics, and other molecular biology techniques.

Prof. Dr. Jinsong Bao
Guest Editor

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Keywords

cereal
rice
wheat
maize
barley
sorghum
millet
molecular markers
genome-wide association studies
genome editing
genome selection
sequencing
molecular selection
transcriptomics
omics
post-translational regulation
starch
protein
lipids
vitamin
phenolics
processing quality
eating quality

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Published Papers (7 papers)

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Research

14 pages, 6075 KiB

Open AccessArticle

Comparative Metabolome and Transcriptome Analysis Reveals the Possible Roles of Rice Phospholipase A Genes in the Accumulation of Oil in Grains

by Huasheng Cao, Rong Gong, Liang Xiong, Fujun Wang, Haiyong Gu, Shuguang Li, Gao He, Shihu Liang, Wenyong Luo and Xianjin Qiu

Int. J. Mol. Sci. 2024, 25(21), 11498; https://doi.org/10.3390/ijms252111498 - 26 Oct 2024

Viewed by 492

Abstract

The phospholipase A (PLA) gene family plays a crucial role in the regulation of plant growth, development and stress response. Although PLA genes have been identified in various plant species, their specific functions and characteristics in oil quality formation of rice grains (Oryza sativa L.) have not been studied yet. Here, we identified and characterized 35 rice PLA genes, which were divided into three subgroups based on gene structures and phylogenetic relationships. These genes are distributed unevenly across 11 rice chromosomes. The promoter sequence of rice PLAs contain multiple plant hormones and stress-related elements. Gene expression analyses in various tissues and under stress conditions indicated that PLAs may be involved in rice growth, development and stress response. In addition, metabolomics, transcriptomics and qRT-PCR analyses between two rice varieties Guang8B (G8B, high oil content) and YueFengB (YFB, low oil content) revealed that the different expressional levels of rice PLA genes were closely related to the differences in the oil content between ‘G8B’ and ‘YFB’ grains. The findings of this study provide potential novel insights into the molecular information of the phospholipase A gene family in rice, and underscore the potential functions of PLA genes in rice oil content accumulation, providing valuable resources for future genetic improvement and breeding strategies. Full article

(This article belongs to the Special Issue Molecular Research for Cereal Grain Quality 2.0)

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12 pages, 1439 KiB

Open AccessArticle

QTL Analysis for Rice Quality-Related Traits and Fine Mapping of qWCR3

by Jun Liu, Hao Zhang, Yingying Wang, Enyu Liu, Huan Shi, Guanjun Gao, Qinglu Zhang, Guangming Lou, Gonghao Jiang and Yuqing He

Int. J. Mol. Sci. 2024, 25(8), 4389; https://doi.org/10.3390/ijms25084389 - 16 Apr 2024

Viewed by 1186

Abstract

The quality of rice, evaluated using multiple quality-related traits, is the main determinant of its market competitiveness. In this study, two japonica rice varieties with significant differences in quality-related traits were used as parents to construct two populations, BC₃F₂ and BC₃F_2:3, with Kongyu131 (KY131) as the recurrent parent. A genetic linkage map was constructed using the BC₃F₂ population based on 151 pairs of SSR/InDel polymorphic markers selected between the parents. Grain-shape-related traits (grain length GL, grain width GW, and length-to-width ratio LWR), chalkiness-related traits (white-core rate WCR, white-belly rate WBR, white-back rate BR, and chalkiness rate CR), and amylose content (AC) were investigated in the two populations in 2017 and 2018. Except for BR and CR, the traits showed similar characteristics with a normal distribution in both populations. Genetic linkage analysis was conducted for these quality-related traits, and a total of 37 QTLs were detected in the two populations. Further validation was performed on the newly identified QTLs with larger effects, and three grain shape QTLs and four chalkiness QTLs were successfully validated in different environments. One repeatedly validated QTL, qWCR3, was selected for fine mapping and was successfully narrowed down to a 100 kb region in which only two genes, LOC_0s03g45210 and LOC_0s03g45320, exhibited sequence variations between the parents. Furthermore, the variation of LOC_Os03g45210 leads to a frameshift mutation and premature protein termination. The results of this study provide a theoretical basis for positional cloning of the qWCR3 gene, thus offering new genetic resources for rice quality improvement. Full article

(This article belongs to the Special Issue Molecular Research for Cereal Grain Quality 2.0)

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19 pages, 8991 KiB

Open AccessArticle

Fine Mapping of Five Grain Size QTLs Which Affect Grain Yield and Quality in Rice

by Yin Zhou, Hanyuan Yang, Enyu Liu, Rongjia Liu, Mufid Alam, Haozhou Gao, Guanjun Gao, Qinglu Zhang, Yanhua Li, Lizhong Xiong and Yuqing He

Int. J. Mol. Sci. 2024, 25(8), 4149; https://doi.org/10.3390/ijms25084149 - 9 Apr 2024

Cited by 3 | Viewed by 1132

Abstract

Grain size is a quantitative trait with a complex genetic mechanism, characterized by the combination of grain length (GL), grain width (GW), length to width ration (LWR), and grain thickness (GT). In this study, we conducted quantitative trait loci (QTL) analysis to investigate the genetic basis of grain size using BC₁F₂ and BC₁F_2:3 populations derived from two indica lines, Guangzhan 63-4S (GZ63-4S) and TGMS29 (core germplasm number W240). A total of twenty-four QTLs for grain size were identified, among which, three QTLs (qGW1, qGW7, and qGW12) controlling GL and two QTLs (qGW5 and qGL9) controlling GW were validated and subsequently fine mapped to regions ranging from 128 kb to 624 kb. Scanning electron microscopic (SEM) analysis and expression analysis revealed that qGW7 influences cell expansion, while qGL9 affects cell division. Conversely, qGW1, qGW5, and qGW12 promoted both cell division and expansion. Furthermore, negative correlations were observed between grain yield and quality for both qGW7 and qGW12. Nevertheless, qGW5 exhibited the potential to enhance quality without compromising yield. Importantly, we identified two promising QTLs, qGW1 and qGL9, which simultaneously improved both grain yield and quality. In summary, our results laid the foundation for cloning these five QTLs and provided valuable resources for breeding rice varieties with high yield and superior quality. Full article

(This article belongs to the Special Issue Molecular Research for Cereal Grain Quality 2.0)

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19 pages, 6693 KiB

Open AccessArticle

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 1 | Viewed by 1506

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, 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, Wx^a, Wx^b, Wxⁱⁿ, Wx^la/mw, and Wx^lv 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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15 pages, 1657 KiB

Open AccessArticle

Genetic Effects Analysis of QTLs for Rice Grain Size Based on CSSL-Z403 and Its Dissected Single and Dual-Segment Substitution Lines

by Guangyi Xu, Keli Deng, Jinjin Yu, Qiaolong Li, Lu Li, Aoni Xiang, Yinghua Ling, Changwei Zhang and Fangming Zhao

Int. J. Mol. Sci. 2023, 24(15), 12013; https://doi.org/10.3390/ijms241512013 - 27 Jul 2023

Cited by 2 | Viewed by 1316

Abstract

Rice chromosomal segment substitution lines (CSSLs) are ideal materials for studying quantitative traits such as grain size. Here, a rice large-grain CSSL-Z403 was identified among progeny of the recipient Xihui18 and the donor Jinhui35 based on molecular marker-assisted selection. Z403 carried 10 substitution segments with average length of 3.01 Mb. Then, a secondary F₂ population derived from a cross between Xihui18 and Z403 was used to map quantitative trait loci (QTL) for grain size. Six QTLs distributed on chromosomes 5, 6, 7, 9 and 12 were detected. Finally four single-segment substitution lines (SSSLs) and two dual-segment substitution lines (DSSLs) carrying these target QTLs were constructed, and 10 novel QTLs were identified by four SSSLs. The large grain of Z403 was controlled at least by qGWT5, qGWT7, qGWT9 and qGWT12, and its grain weight was influenced through grain length QTL such as qGL5, qGL6, qGL9 and qGL12, as well as grain width QTL such as qGW5, qGW7, qGW9 and qGW12. Among 16 QTLs, four QTLs including qGL6, etc., might be novel compared with the reported documents. Again, positive or less negative epistatic effects between two non-allelic QTLs (additive effect > 0) may assist screening the genotype with larger grain size in further selection. Full article

(This article belongs to the Special Issue Molecular Research for Cereal Grain Quality 2.0)

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15 pages, 2676 KiB

Open AccessArticle

Conjunctive Analyses of BSA-Seq and BSR-Seq to Identify Candidate Genes Controlling the Black Lemma and Pericarp Trait in Barley

by Yajie Liu, Pengzheng Chen, Wenshuo Li, Xinchun Liu, Guowu Yu, Hui Zhao, Shuhua Zeng, Mao Li, Genlou Sun and Zongyun Feng

Int. J. Mol. Sci. 2023, 24(11), 9473; https://doi.org/10.3390/ijms24119473 - 30 May 2023

Cited by 7 | Viewed by 2475

Abstract

Black barley seeds are a health-beneficial diet resource because of their special chemical composition and antioxidant properties. The black lemma and pericarp (BLP) locus was mapped in a genetic interval of 0.807 Mb on chromosome 1H, but its genetic basis remains unknown. In this study, targeted metabolomics and conjunctive analyses of BSA-seq and BSR-seq were used to identify candidate genes of BLP and the precursors of black pigments. The results revealed that five candidate genes, purple acid phosphatase, 3-ketoacyl-CoA synthase 11, coiled-coil domain-containing protein 167, subtilisin-like protease, and caffeic acid-O-methyltransferase, of the BLP locus were identified in the 10.12 Mb location region on the 1H chromosome after differential expression analysis, and 17 differential metabolites, including the precursor and repeating unit of allomelanin, were accumulated in the late mike stage of black barley. Phenol nitrogen-free precursors such as catechol (protocatechuic aldehyde) or catecholic acids (caffeic, protocatechuic, and gallic acids) may promote black pigmentation. BLP can manipulate the accumulation of benzoic acid derivatives (salicylic acid, 2,4-dihydroxybenzoic acid, gallic acid, gentisic acid, protocatechuic acid, syringic acid, vanillic acid, protocatechuic aldehyde, and syringaldehyde) through the shikimate/chorismite pathway other than the phenylalanine pathway and alter the metabolism of the phenylpropanoid-monolignol branch. Collectively, it is reasonable to infer that black pigmentation in barley is due to allomelanin biosynthesis in the lemma and pericarp, and BLP regulates melanogenesis by manipulating the biosynthesis of its precursors. Full article

(This article belongs to the Special Issue Molecular Research for Cereal Grain Quality 2.0)

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17 pages, 6080 KiB

Open AccessArticle

The Landscapes of Gluten Regulatory Network in Elite Wheat Cultivars Contrasting in Gluten Strength

by Jiajun Liu, Dongsheng Li, Peng Zhu, Shi Qiu, Kebing Yao, Yiqing Zhuang, Chen Chen, Guanqing Liu, Mingxing Wen, Rui Guo, Weicheng Yao, Yao Deng, Xueyi Shen and Tao Li

Int. J. Mol. Sci. 2023, 24(11), 9447; https://doi.org/10.3390/ijms24119447 - 29 May 2023

Viewed by 1908

Abstract

Yangmai-13 (YM13) is a wheat cultivar with weak gluten fractions. In contrast, Zhenmai-168 (ZM168) is an elite wheat cultivar known for its strong gluten fractions and has been widely used in a number of breeding programs. However, the genetic mechanisms underlying the gluten signatures of ZM168 remain largely unclear. To address this, we combined RNA-seq and PacBio full-length sequencing technology to unveil the potential mechanisms of ZM168 grain quality. A total of 44,709 transcripts were identified in Y13N (YM13 treated with nitrogen) and 51,942 transcripts in Z168N (ZM168 treated with nitrogen), including 28,016 and 28,626 novel isoforms in Y13N and Z168N, respectively. Five hundred and eighty-four differential alternative splicing (AS) events and 491 long noncoding RNAs (lncRNAs) were discovered. Incorporating the sodium-dodecyl-sulfate (SDS) sedimentation volume (SSV) trait, both weighted gene coexpression network analysis (WGCNA) and multiscale embedded gene coexpression network analysis (MEGENA) were employed for network construction and prediction of key drivers. Fifteen new candidates have emerged in association with SSV, including 4 transcription factors (TFs) and 11 transcripts that partake in the post-translational modification pathway. The transcriptome atlas provides new perspectives on wheat grain quality and would be beneficial for developing promising strategies for breeding programs. Full article

(This article belongs to the Special Issue Molecular Research for Cereal Grain Quality 2.0)

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