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Molecular Research for Cereal Grain Quality 2.0

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: 30 June 2024 | Viewed by 4801

Special Issue Editor

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

Manuscript Submission Information

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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

Published Papers (4 papers)

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Research

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
Viewed by 297
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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15 pages, 1657 KiB  
Article
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 1 | Viewed by 784
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 [...] Read more.
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  
Article
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 2 | Viewed by 1669
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 [...] Read more.
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  
Article
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 1290
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 [...] Read more.
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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