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Molecular Genetics and Functional Genomics for the Breeding of Cereal...
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Molecular Genetics and Functional Genomics for the Breeding of Cereal Crops

A special issue of Agriculture (ISSN 2077-0472). This special issue belongs to the section "Crop Production".

Deadline for manuscript submissions: closed (30 June 2023) | Viewed by 22076

Special Issue Editors

Prof. Dr. Xingguo Ye

E-Mail Website
Guest Editor
Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Interests: wheat; genetic transformation; gene editing; tissue and chromosome engineering; molecular breeding
Dr. Ke Wang

E-Mail Website
Guest Editor
Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Interests: wheat; genetic transformation; gene editing; molecular genetics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Cereals including rice, maize, wheat, barley, millet, buckwheat, sorghum, and oats are widely planted food crops across the globe, and their growing production has great significance for ensuring worldwide food security and social stability. Breeding new varieties of these cereal crops with desirable agronomic, quality, biotic and abiotic traits is one of the key strategies for increasing yield. With the development of genome sequencing and gene-editing technologies, the genetic improvement of cereal crops has been greatly accelerated in the past ten years. Especially, efficient genetic transformation systems have been established in maize, indica rice and wheat by using plant-regeneration-related genes (WUS2, BBM and GRF-GIF) or modifying culture and selection regimes (PureWheat). Model genotypes of rice and millet with dwarfing plant heights, short growth periods, and high transformation efficiency have been created for genetic study. Many important germplasms or mutants have been developed, and many genes of interest have been dissected for functional regulation in rice, maize, wheat, barley, sorghum and millet by applying transgenic and CRISPR/Cas9 techniques. Additionally, more convenient molecular markers have been designed and employed in the breeding of cereal crops. On the whole, optimal progress has been achieved in cereal crops regarding molecular genetics, functional genomics, transformation, gene editing, and marker-assisted selective breeding. It is necessary to organize a Special Issue in this journal to report some novel results and opinions related to the aspects aforementioned in cereal crops.

This Special Issue will publish recent research that describes the state of the art in research and development on solutions in molecular genetics, functional genomics and genetic modification for the improvement of cereal crops.

Prof. Dr. Xingguo Ye
Dr. Ke Wang
Guest Editors

Manuscript Submission Information

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Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • cereal crops
  • functional assessment
  • gene editing
  • genetic improvement
  • genetic transformation
  • model genotypes
  • molecular markers

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Published Papers (8 papers)

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Research

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11 pages, 3874 KiB  
Article
Gene Locus Mapping and Candidate Gene Screening for Branched Spike and Its Associated Traits of the Ynbs Mutant in Barley
by Hongbin Zhou, Junyu He, Mengyue Wang, Xintian Wang and Shengwei Chen
Agriculture 2023, 13(10), 1934; https://doi.org/10.3390/agriculture13101934 - 3 Oct 2023
Viewed by 1649
Abstract
The Ynbs (Yunnan branched-spike) mutant of naked barley with a branched spike displays some special traits, such as more degenerated multiple spikelets per spike and florets per multiple spikelets and a lower seed-setting rate. However, there is still a lack of understanding the [...] Read more.
The Ynbs (Yunnan branched-spike) mutant of naked barley with a branched spike displays some special traits, such as more degenerated multiple spikelets per spike and florets per multiple spikelets and a lower seed-setting rate. However, there is still a lack of understanding the loci of the trait. In the present study, the Ynbs mutant was crossed with Baodamai8 to breed F2 and F2:5 populations. The F2 and F2:5 populations were successively employed to map the loci for a branched spike, triplicate (or multiple) spikelet number per spike (T(M)SNS), degenerated triplicate (or multiple) spikelet number per spike (DT(M)SNS) and floret number per triplicate (or multiple) spikelet (FNT(M)S). The genetic interval mapped through the F2:5 population was flanked by markers HvSSR4 and HVSSR20, and, within that, mapped through the F2 population. The genetic distance of the branched-spike locus to HVSSR20 locus, T(M)SNS, FNT(M)S), and DT(M)SNS is 1.86 centiMorgan (cM), 0.27 cM, and 0.73 cM, respectively. The Morex genome sequence defined by markers HvSSR4 and HVSSR20 harbored 18 genes, among which HORVU.MOREX.r3.2HG0114260 belonged to the AP2/ERF domain transcription factor gene superfamily. In the Ynbs mutant, the C base at site 232 of the code domain sequence of the gene was substituted with T, leading to the substitution of arginine with cysteine at site 78 in the DNA-binding domain of the encoded protein. The gene harbors a new allele mutant in the Ynbs mutant and exhibits a pleiotropy in the development of a branched spike, spikelet, and floret. The results provide valuable information for elucidating the development mechanism of barley young spike. Full article
(This article belongs to the Special Issue Molecular Genetics and Functional Genomics for the Breeding of Cereal Crops)
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10 pages, 4606 KiB  
Article
Development of KASP and SSR Markers for PmQ, a Recessive Gene Conferring Powdery Mildew Resistance in Wheat Landrace Qingxinmai
by Habteab Goitom Gebremedhin, Yahui Li, Jinghuang Hu, Dan Qiu, Qiuhong Wu, Hongjun Zhang, Li Yang, Yang Zhou, Yijun Zhou, Zhiyong Liu, Peng Zhang and Hongjie Li
Agriculture 2022, 12(9), 1344; https://doi.org/10.3390/agriculture12091344 - 31 Aug 2022
Viewed by 1946
Abstract
A recessive gene PmQ conferring powdery mildew resistance was previously localized on the long arm of chromosome 2B in winter wheat landrace Qingxinmai. Breeder-friendly molecular markers are necessary for introgressing this gene into adapted wheat backgrounds for developing disease-resistant wheat cultivars. Three Kompetitive [...] Read more.
A recessive gene PmQ conferring powdery mildew resistance was previously localized on the long arm of chromosome 2B in winter wheat landrace Qingxinmai. Breeder-friendly molecular markers are necessary for introgressing this gene into adapted wheat backgrounds for developing disease-resistant wheat cultivars. Three Kompetitive allele-specific PCR (KASP) markers were developed and validated based on SNP variants detected by Bulked segregant analysis-RNA-Seq (BSR-Seq) analysis using a recombinant inbred population derived from cross Qingxinmai × 041133. Two polymorphic SSR markers were also developed from the motifs in the Chinese Spring reference genome sequences of the target genomic region. Those markers were incorporated into a more saturated genetic linkage map for PmQ. The two flanking markers, Xicsq405 and Xicsk18, are 1.1 and 0.9 cM from PmQ, respectively. The KASP marker Xicsk19 produced unique amplification pattern in 158 out of 160 wheat cultivars or breeding lines. This marker with the gene-linked SSR markers Xicsqc, Xicsqd and Xicsq405 provides an efficient means in molecular marker-assisted selection for PmQ in wheat breeding. The corresponding genomic region of PmQ in the Chinese Spring reference genome has a conserved synteny with the genomes of sequenced wheat cultivars and Triticum durum, T. diccocoides, T. uratu, and barley. The annotation of the two genes, TraesCS2B01G517400.1 and TraesCS2B01G517700.1, associated with plant defense against pathogens placed a start for cloning PmQ. Full article
(This article belongs to the Special Issue Molecular Genetics and Functional Genomics for the Breeding of Cereal Crops)
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16 pages, 2680 KiB  
Article
DELAYED HEADING DATE3, Encoding a Heat Shock Transcription Factor, Delays Flowering Time and Improves Yield in Rice (Oryza sativa L.)
by Tianzhen Liu, Huan Zhang, Liang Zhou, Xin Zhang, Chunlei Zhou, Shuai Li, Zhijun Cheng, Xiuping Guo, Shanshan Zhu and Jianmin Wan
Agriculture 2022, 12(7), 1022; https://doi.org/10.3390/agriculture12071022 - 14 Jul 2022
Viewed by 2281
Abstract
Heading date is an essential agronomic trait that affects adaptability and yield in rice (Oryza sativa). HSFs (heat shock transcription factors) are a type of transcription factor that responds to environmental stress in organisms. The relationship between the heading date and [...] Read more.
Heading date is an essential agronomic trait that affects adaptability and yield in rice (Oryza sativa). HSFs (heat shock transcription factors) are a type of transcription factor that responds to environmental stress in organisms. The relationship between the heading date and HSFs has been seldom reported so far. Here, we identified a new heat shock transcription factor, named DELAYED HEADING DATE3 (DHD3), which can significantly delay the heading date by about 14 days and provide improvements of about 77% potential yield in rice. DHD3 protein is localized in the nucleus and has weak transactivation activity. DHD3 delays the heading date by significantly suppressing Hd3a and RFT1 expression under long-day (LD) and short-day (SD) conditions. Furthermore, the low-temperature condition greatly enhances the delay effect of DHD3 on the heading date (from 16.1% to more than 89.3%). We propose that DHD3 may involve the temperature-regulated signaling pathway of flowering time in rice and has the potential to improve crop yield. Full article
(This article belongs to the Special Issue Molecular Genetics and Functional Genomics for the Breeding of Cereal Crops)
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16 pages, 3587 KiB  
Article
Effects of TaMTL-Edited Mutations on Grain Phenotype and Storage Component Composition in Wheat
by Huali Tang, Shuangxi Zhang, Mei Yu, Ke Wang, Yang Yu, Yuliang Qiu, Yanan Chang, Zhishan Lin, Lipu Du, Daolin Fu, Zichao Li and Xingguo Ye
Agriculture 2022, 12(5), 587; https://doi.org/10.3390/agriculture12050587 - 22 Apr 2022
Cited by 3 | Viewed by 2138
Abstract
Wheat nutrition and processing-quality are primarily based on the endosperm ingredients. However, the effect of embryos on grain traits and components remains unclear. In this study, we found that in the cross-pollinated and self-pollinated progenies of the four wheat mtl mutants (mtl [...] Read more.
Wheat nutrition and processing-quality are primarily based on the endosperm ingredients. However, the effect of embryos on grain traits and components remains unclear. In this study, we found that in the cross-pollinated and self-pollinated progenies of the four wheat mtl mutants (mtl-A, mtl-AD, mtl-BD, and mtl-ABD) the haploid induction rates were 0–15.6% and 0–14.1%, and the embryo abortion rates were 0–27.4% and 0–24.1%, respectively, in which mtl-A had no effect on haploid induction and embryo development. The embryoless grains (ELG) were comparable to the normal grains (NG) from mtl-AD, mtl-BD, and mtl-ABD in grain length, grain width and thousand-kernel weight, but the grain traits were significantly less than those in NG from mutant mtl-A. During grain filling period, mtl-ABD had similar ELG ratio and amount of starch granule (SG) and protein body (PB) in ELG and NG. At maturity stage, the morphological features of A-type and B-type SG in ELG were similar to those in NG in mtl mutants; however, amylose, gliadin, and glutenin contents were higher in ELG, and total starch, albumin and globulin contents were higher in NG. Our results clarified the effect of the wheat mtl mutants on haploid induction and grain traits and nutrition composition in this crop, and provided new clues for studying the development of embryo and endosperm and their interaction in plants. Full article
(This article belongs to the Special Issue Molecular Genetics and Functional Genomics for the Breeding of Cereal Crops)
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13 pages, 2910 KiB  
Article
Dynamic Resistant Starch Accumulation in Contrasting Wheat Genotypes Highlights the Lipid Metabolic Pathway Related to Resistant Starch Synthesis
by Hong-Pan Wang, Hai-Ya Cai, Jing-Huan Zhu, Xia Wei, Shuo Zhang, Gang Liu, Yong-Gang He, Bo Li, Le Xu, Chun-Hai Jiao, Wei Hua and Yan-Hao Xu
Agriculture 2022, 12(2), 308; https://doi.org/10.3390/agriculture12020308 - 21 Feb 2022
Cited by 5 | Viewed by 2712
Abstract
Resistant starch (RS) shows several health benefits. Enhancing the RS content of wheat is of major commercial importance. However, knowledge regarding the RS synthesis mechanism in wheat remains limited. In this study, the dynamic accumulation of RS during the filling process in two [...] Read more.
Resistant starch (RS) shows several health benefits. Enhancing the RS content of wheat is of major commercial importance. However, knowledge regarding the RS synthesis mechanism in wheat remains limited. In this study, the dynamic accumulation of RS during the filling process in two wheat (Triticum aestivum L.) genotypes with contrasting RS contents (H242, high RS content; H189, low RS content) were investigated. The results demonstrate that beyond 25 days after pollination (DAP), the RS content of H189 was relatively stable, but that of H242 continued to increase. Secondary accumulation was observed in the high-RS-content wheat genotype. A comparative transcriptome analysis between H242 and H189 at 20 DAP and 35 DAP showed that the differentially expressed genes were mainly involved in glycerolipid metabolism, glycerophospholipid metabolism and glucuronate interconversions. Furthermore, weighted gene coexpression network analysis suggested that lipid metabolic pathways such as the glycerophospholipid metabolism pathway might be involved in RS synthesis, and lipid-related genes upregulated beyond 25 DAP resulted in RS secondary accumulation. This work provides insight into the characteristics and mechanisms of RS synthesis. Full article
(This article belongs to the Special Issue Molecular Genetics and Functional Genomics for the Breeding of Cereal Crops)
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14 pages, 2055 KiB  
Article
Genome-Wide Association Study Reveals Genetic Basis of Trace Elements Accumulation in Maize Kernels
by Fucheng Zhao, Nan Wang, Fei Bao, Guangwu Zhao, Liquan Jing, Guiyue Wang, Qinghui Han, Zhuanfang Hao and Bin Chen
Agriculture 2022, 12(2), 262; https://doi.org/10.3390/agriculture12020262 - 11 Feb 2022
Cited by 5 | Viewed by 2332
Abstract
Clarifying the genetic basis of trace element accumulation is of great significance to breed new maize varieties with high quality. In this study, an integrated variant map with 1.25 million (M) SNPs and 489 inbred lines was used for a genome-wide association study [...] Read more.
Clarifying the genetic basis of trace element accumulation is of great significance to breed new maize varieties with high quality. In this study, an integrated variant map with 1.25 million (M) SNPs and 489 inbred lines was used for a genome-wide association study on the accumulation of iron (Fe), manganese (Mn), copper (Cu), zinc (Zn), cadmium (Cd) and Arsenic (As) in maize kernels. Seventeen SNPs linked with six genes were overlapped by different trace elements. After further analysis, 65 SNPs located in 28 genes with a p-value lower than 10−10 were associated with Cd content by genome-wide association studies (GWAS). There was a 3.1-fold difference in Cd content between different groups, which was divided by SNP haplotype in chr2.S_160782359, chr2.S_161045498 and chr2.S_161273716. The amino acid sequences of GRMZM2G150608 and GRMZM2G051367 only shared 68.85% and 88.16% similarity between B73 and Mo17, and the Cd content of Mo17 was 2.2-fold that of B73. In addition, 19 lines with higher contents of Fe, Zn, Cu, Mn and fewer contents of As and Cd were screened from GWAS associated populations. This study will lay a foundation for revealing the molecular mechanism of trace element accumulation in maize kernels and provide candidate genes for breeding new maize varieties with high nutritional quality. Full article
(This article belongs to the Special Issue Molecular Genetics and Functional Genomics for the Breeding of Cereal Crops)
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15 pages, 2227 KiB  
Article
Identification of Drought-Resistant Genes in Shanlan Upland Rice
by Xiaoling Niu, Nanxin Zhai, Xinsen Yang, Meng Su, Caiyue Liu, Liu Wang, Pengzheng Qu, Wuge Liu, Qianhua Yuan and Xinwu Pei
Agriculture 2022, 12(2), 150; https://doi.org/10.3390/agriculture12020150 - 21 Jan 2022
Cited by 7 | Viewed by 3348
Abstract
Shanlan upland rice is a kind of upland rice and is suitable for planting in the mountains and in hilly terrain. It is mainly found in China’s Hainan province. To discover the drought-resistant genes in Shanlan upland rice, two representative varieties—Baishanuo (BSN) and [...] Read more.
Shanlan upland rice is a kind of upland rice and is suitable for planting in the mountains and in hilly terrain. It is mainly found in China’s Hainan province. To discover the drought-resistant genes in Shanlan upland rice, two representative varieties—Baishanuo (BSN) and Dongfang Manpoxiang (MPX)—were selected for transcriptome sequencing, after which gene expression analysis was used to confirm their gene expression patterns. The results demonstrated that 2791 and 829 differentially expressed genes (DEGs) were identified for each variety, including 184 and 58 transcriptional factors, respectively. Expression analysis demonstrated that some genes with unknown functions, such as Os10g0505900, were highly expressed under drought stress treatment. The transcriptomic data and digital gene expression profiling data obtained in this study provide a basis for studying the drought-resistant mechanism in Shanlan upland rice. Full article
(This article belongs to the Special Issue Molecular Genetics and Functional Genomics for the Breeding of Cereal Crops)
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Review

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13 pages, 774 KiB  
Review
Susceptibility Is New Resistance: Wheat Susceptibility Genes and Exploitation in Resistance Breeding
by Mengmeng Li, Zige Yang and Cheng Chang
Agriculture 2022, 12(9), 1419; https://doi.org/10.3390/agriculture12091419 - 8 Sep 2022
Cited by 8 | Viewed by 3678
Abstract
Adapted pathogens and pests seriously threaten global wheat production. During pathogen and pest infections, wheat susceptibility (S) genes are exploited to support the compatibility of wheat with pathogens and pests. A plethora of wheat S genes were recently identified and revealed [...] Read more.
Adapted pathogens and pests seriously threaten global wheat production. During pathogen and pest infections, wheat susceptibility (S) genes are exploited to support the compatibility of wheat with pathogens and pests. A plethora of wheat S genes were recently identified and revealed to regulate multiple processes, including pathogen (pre)penetration, plant immunity, pathogen sustenance, and pest feeding. The inactivation of some S genes via newly developed genome editing and TILLING techniques could reduce compatibility and confer broad-spectrum and durable resistance, which provide a new avenue for wheat resistance improvement. In this review, we summarized recent advances in the characterization of wheat S genes and highlighted their multifaceted roles in facilitating compatible interactions of wheat with adapted pathogens and pests. Current strategies, limitations, and future directions in exploiting S genes in wheat resistance breeding are discussed. Full article
(This article belongs to the Special Issue Molecular Genetics and Functional Genomics for the Breeding of Cereal Crops)
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