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Breeding and Genetics of Rice
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Breeding and Genetics of Rice

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: closed (20 January 2024) | Viewed by 7106

Special Issue Editor

Dr. Changhui Sun

E-Mail Website
Guest Editor
State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
Interests: rice; gene clone; gene function analysis; yield; heading date

Special Issue Information

Dear Colleagues,

Rice feeds more than half of the world’s population. There have been two major yield breakthroughs in rice breeding in history: the Green Revolution in the 1960s and hybrid technology in the 1970s. Since then, there has been no major breakthrough in rice yields. With the advancement of molecular biology research and the rapid development of biotechnology, modern biotechnology offers another possibility of breakthroughs in rice yield. The priority topics of this issue are the characterization and application of useful traits’ genes or QLTs, such as yield potential and quality improvement, stress resistance, heading date, and so on. Creating new rice materials with high yield, high quality, multiple resistance, and wide adaptation using transgenic or gene editing techniques and studying these materials at the phenotypic, physiological, molecular, and genetic levels are welcomed. On the other hand, with the rapid development of the rice genome field, the analysis and application of genomics-based superior allelic variants are also welcomed.

Dr. Changhui Sun
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

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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

  • rice breeding
  • yield
  • quality
  • stress resistance
  • heading date
  • gene/QTL cloning
  • gene function analysis
  • transgenic or gene editing techniques
  • genome-wide association analysis
  • superior allelic variation

Published Papers (6 papers)

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Research

18 pages, 6469 KiB  
Article
Mapping of Candidate Genes for Nitrogen Uptake and Utilization in Japonica Rice at Seedling Stage
by Ning Chen, Tianze Ma, Sijia Xia, Chengxin Li, Yinuo Liu, Jiaqi Wang, Guize Qu, Hualong Liu, Hongliang Zheng, Luomiao Yang, Detang Zou, Jingguo Wang and Wei Xin
Genes 2024, 15(3), 327; https://doi.org/10.3390/genes15030327 - 02 Mar 2024
Viewed by 945
Abstract
Nitrogen (N) is one of the essential nutrients for the growth and development of crops. The adequate application of N not only increases the yield of crops but also improves the quality of agricultural products, but the excessive application of N can cause [...] Read more.
Nitrogen (N) is one of the essential nutrients for the growth and development of crops. The adequate application of N not only increases the yield of crops but also improves the quality of agricultural products, but the excessive application of N can cause many adverse effects on ecology and the environment. In this study, genome-wide association analysis (GWAS) was performed under low- and high-N conditions based on 788,396 SNPs and phenotypic traits relevant to N uptake and utilization (N content and N accumulation). A total of 75 QTLs were obtained using GWAS, which contained 811 genes. Of 811 genes, 281 genes showed different haplotypes, and 40 genes had significant phenotypic differences among different haplotypes. Of these 40 genes, 5 differentially expressed genes (Os01g0159250, Os02g0618200, Os02g0618400, Os02g0630300, and Os06g0619000) were finally identified as the more valuable candidate genes based on the transcriptome data sequenced from Longjing31 (low-N-tolerant variety) and Songjing 10 (low-N-sensitive variety) under low- and high-N treatments. These new findings enrich the genetic resources for N uptake and utilization in rice, as well as lay a theoretical foundation for improving the efficiency of N uptake and utilization in rice. Full article
(This article belongs to the Special Issue Breeding and Genetics of Rice)
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17 pages, 3569 KiB  
Article
Effect of Fat Content on Rice Taste Quality through Transcriptome Analysis
by Jie Guo, Xinqiao Zhou, Dagang Chen, Ke Chen, Chanjuan Ye, Juan Liu, Shaolong Liu, Youding Chen, Guorong Chen and Chuanguang Liu
Genes 2024, 15(1), 81; https://doi.org/10.3390/genes15010081 - 09 Jan 2024
Viewed by 1106
Abstract
Rice is an important crop in the word, and fat is one of the main important nutrient components of rice. The lipid content and fatty acid composition of grains significantly influences the quality of rice. In this study, 94 homozygous recombination inbred lines [...] Read more.
Rice is an important crop in the word, and fat is one of the main important nutrient components of rice. The lipid content and fatty acid composition of grains significantly influences the quality of rice. In this study, 94 homozygous recombination inbred lines (RILs) were developed and the crude fat content of them displayed a normal distribution ranging from 0.44% to 2.62%. Based on their taste quality, a positive association between fat content and eating quality was revealed. Then, two lines (FH and FL) were selected with similar agronomic characteristics and different lipid content and taste quality for RNA sequencing analysis, and a total of 619 differentiable expressed genes were detected, primarily enriched in metabolic pathways such as starch and sucrose metabolism, fatty acid metabolism, and amino acid metabolism. The expression of two genes related to fatty acid synthesis and elongation was significantly up-regulated, while the expression of three genes related to fatty acid degradation was significantly down-regulated in FH grains. By using liquid chromatography, the relative levels of palmitic acid and oleic acid were discovered significantly higher in FH grains. Additionally, the comparative genomic analysis was conducted to visualize genomic differences of five genes. Ultimately, two genes (Os07g0417200 and Os12g0102100) were selected to be the key gene to affect the lipid metabolism, especially for the synthesis of unsaturated fatty acids, significantly changing the eating quality of rice. These results provide a theoretical basis for improving the taste quality of rice. Full article
(This article belongs to the Special Issue Breeding and Genetics of Rice)
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15 pages, 2223 KiB  
Article
Identification of Superior Haplotypes and Haplotype Combinations for Grain Size- and Weight-Related Genes for Breeding Applications in Rice (Oryza sativa L.)
by Gang Liu, Dongfeng Qiu, Yuxia Lu, Yan Wu, Xuesong Han, Yaru Jiao, Tingbao Wang, Jinsong Yang, Aiqing You, Jianguo Chen and Zaijun Zhang
Genes 2023, 14(12), 2201; https://doi.org/10.3390/genes14122201 - 12 Dec 2023
Viewed by 842
Abstract
The identification of superior haplotypes and haplotype combinations is essential for haplotype-based breeding (HBB), which provides selection targets for genomics-assisted breeding. In this study, genotypes of 42 functional genes in rice were analyzed by targeted capture sequencing in a panel of 180 Indica [...] Read more.
The identification of superior haplotypes and haplotype combinations is essential for haplotype-based breeding (HBB), which provides selection targets for genomics-assisted breeding. In this study, genotypes of 42 functional genes in rice were analyzed by targeted capture sequencing in a panel of 180 Indica rice accessions. In total, 69 SNPs/Indels in seven genes were detected to be associated with grain length (GL), grain width (GW), ratio of grain length–width (L/W) and thousand-grain weight (TGW) using candidate gene-based association analysis, including BG1 and GS3 for GL, GW5 for GW, BG1 and GW5 for L/W, and AET1, SNAC1, qTGW3, DHD1 and GW5 for TGW. Furthermore, two haplotypes were identified for each of the seven genes according to these associated SNPs/Indels, and the amount of genetic variation explained by different haplotypes ranged from 3.24% to 27.66%. Additionally, three, three and eight haplotype combinations for GL, L/W and TGW explained 25.38%, 5.5% and 22.49% of the total genetic variation for each trait, respectively. Further analysis showed that Minghui63 had the superior haplotype combination Haplotype Combination 4 (HC4) for TGW. The most interesting finding was that some widely used restorer lines derived from Minghui63 also have the superior haplotype combination HC4, and our breeding varieties and lines using the haplotype-specific marker panel also confirmed that the TGW of the lines was much higher than that of their sister lines without HC4, suggesting that TGW-HC4 is the superior haplotype combination for TGW and can be utilized in rice breeding. Full article
(This article belongs to the Special Issue Breeding and Genetics of Rice)
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13 pages, 2219 KiB  
Article
Rapid Visual Detection of High Nitrogen-Use Efficiency Gene OsGRF4 in Rice (Oryza sativa L.) Using Loop-Mediated Isothermal Amplification Method
by Yonghang Tian, Wenwei Ye, Xiangshuai Liang, Peizhou Xu, Xianjun Wu, Xiangdong Fu, Yaoxian Chin and Yongxiang Liao
Genes 2023, 14(10), 1850; https://doi.org/10.3390/genes14101850 - 23 Sep 2023
Viewed by 995
Abstract
The GROWTH-REGULATING FACTOR4 (OsGRF4) allele is an important target for the development of new high nitrogen-use efficiency (NUE) rice lines that would require less fertilizers. Detection of OsGRF4 through PCR (polymerase chain reaction)-based assay is cumbersome and needs advanced laboratory skills and [...] Read more.
The GROWTH-REGULATING FACTOR4 (OsGRF4) allele is an important target for the development of new high nitrogen-use efficiency (NUE) rice lines that would require less fertilizers. Detection of OsGRF4 through PCR (polymerase chain reaction)-based assay is cumbersome and needs advanced laboratory skills and facilities. Hence, a method for conveniently and rapidly detecting OsGRF4 on-field is a key requirement for further research and applications. In this study, we employed cleaved amplified polymorphic sequences (CAPs) and loop-mediated isothermal amplification (LAMP) techniques to develop a convenient visual detection method for high NUE gene OsGRF4NM73 (OsGRF4 from the rice line NM73). The TC→AA mutation at 1187–1188 bp loci was selected as the target sequence for the OsGRF4NM73 allele. We further employed this method of identification in 10 rice varieties that carried the OsGRF4 gene and results revealed that one variety (NM73) carries the target OsGRF4NM73 allele, while other varieties did not possess the osgrf4 genotype. The optimal LAMP reaction using hydroxynaphthol blue (HNB), a chromogenic indicator, was carried out at 65 °C for 60 min, and the presence of OsGRF4NM73 allele was confirmed by color changes from violet to sky blue. The results of this study showed that the LAMP method can be conveniently and accurately used to detect the OsGRF4NM73 gene in rice. Full article
(This article belongs to the Special Issue Breeding and Genetics of Rice)
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17 pages, 3436 KiB  
Article
Loss of a Premature Stop Codon in the Rice Wall-Associated Kinase 91 (WAK91) Gene Is a Candidate for Improving Leaf Sheath Blight Disease Resistance
by Noor Al-Bader, Austin Meier, Matthew Geniza, Yamid Sanabria Gongora, James Oard and Pankaj Jaiswal
Genes 2023, 14(9), 1673; https://doi.org/10.3390/genes14091673 - 24 Aug 2023
Cited by 5 | Viewed by 1238
Abstract
Leaf sheath blight disease (SB) of rice caused by the soil-borne fungus Rhizoctonia solani results in 10–30% global yield loss annually and can reach 50% under severe outbreaks. Many disease resistance genes and receptor-like kinases (RLKs) are recruited early on by the host [...] Read more.
Leaf sheath blight disease (SB) of rice caused by the soil-borne fungus Rhizoctonia solani results in 10–30% global yield loss annually and can reach 50% under severe outbreaks. Many disease resistance genes and receptor-like kinases (RLKs) are recruited early on by the host plant to respond to pathogens. Wall-associated receptor kinases (WAKs), a subfamily of receptor-like kinases, have been shown to play a role in fungal defense. The rice gene WAK91 (OsWAK91), co-located in the major SB resistance QTL region on chromosome 9, was identified by us as a candidate in defense against rice sheath blight. An SNP mutation T/C in the WAK91 gene was identified in the susceptible rice variety Cocodrie (CCDR) and the resistant line MCR010277 (MCR). The consequence of the resistant allele C is a stop codon loss, resulting in an open reading frame with extra 62 amino acid carrying a longer protein kinase domain and additional phosphorylation sites. Our genotype and phenotype analysis of the parents CCDR and MCR and the top 20 individuals of the double haploid SB population strongly correlate with the SNP. The susceptible allele T is present in the japonica subspecies and most tropical and temperate japonica lines. Multiple US commercial rice varieties with a japonica background carry the susceptible allele and are known for SB susceptibility. This discovery opens the possibility of introducing resistance alleles into high-yielding commercial varieties to reduce yield losses incurred by the sheath blight disease. Full article
(This article belongs to the Special Issue Breeding and Genetics of Rice)
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17 pages, 4309 KiB  
Article
OsPMS1 Mutation Enhances Salt Tolerance by Suppressing ROS Accumulation, Maintaining Na+/K+ Homeostasis, and Promoting ABA Biosynthesis
by Wang-Qing Li, Wen-Jie Zheng, Yan Peng, Ye Shao, Ci-Tao Liu, Jin Li, Yuan-Yi Hu, Bing-Ran Zhao and Bi-Gang Mao
Genes 2023, 14(8), 1621; https://doi.org/10.3390/genes14081621 - 14 Aug 2023
Cited by 2 | Viewed by 1274
Abstract
World-wide, rice (Oryza sativa L.) is an important food source, and its production is often adversely affected by salinity. Therefore, to ensure stable rice yields for global food security, it is necessary to understand the salt tolerance mechanism of rice. The present [...] Read more.
World-wide, rice (Oryza sativa L.) is an important food source, and its production is often adversely affected by salinity. Therefore, to ensure stable rice yields for global food security, it is necessary to understand the salt tolerance mechanism of rice. The present study focused on the expression pattern of the rice mismatch repair gene post-meiotic segregation 1 (OsPMS1), studied the physiological properties and performed transcriptome analysis of ospms1 mutant seedlings in response to salt stress. Under normal conditions, the wild-type and ospms1 mutant seedlings showed no significant differences in growth and physiological indexes. However, after exposure to salt stress, compared with wild-type seedlings, the ospms1 mutant seedlings exhibited increased relative water content, relative chlorophyll content, superoxide dismutase (SOD) activity, K+ and abscisic acid (ABA) content, and decreased malondialdehyde (MDA) content, Na+ content, and Na+/K+ ratio, as well as decreased superoxide anion (O2−) and hydrogen peroxide (H2O2) accumulation. Gene ontology (GO) analysis of the differentially expressed genes (DEGs) of ospms1 mutant seedlings treated with 0 mM and 150 mM NaCl showed significant enrichment in biological and cytological processes, such as peroxidase activity and ribosomes. The Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway analysis showed that the DEGs specifically enriched ascorbate and aldarate metabolism, flavone and flavonol biosynthesis, and glutathione metabolism pathways. Further quantitative real-time reverse transcription-PCR (qRT-PCR) analysis revealed significant changes in the transcription levels of genes related to abscisic acid signaling (OsbZIP23, OsSAPK6, OsNCED4, OsbZIP66), reactive oxygen scavenging (OsTZF1, OsDHAR1, SIT1), ion transport (OsHAK5), and osmoregulation (OsLEA3-2). Thus, the study’s findings suggest that the ospms1 mutant tolerates salt stress at the seedling stage by inhibiting the accumulation of reactive oxygen species, maintaining Na+ and K+ homeostasis, and promoting ABA biosynthesis. Full article
(This article belongs to the Special Issue Breeding and Genetics of Rice)
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