scholarly journals FLOURY ENDOSPERM19 encoding a class I glutamine amidotransferase affects grain quality in rice

2021 ◽  
Author(s):  
Guangming Lou ◽  
Pingli Chen ◽  
Hao Zhou ◽  
Pingbo Li ◽  
Jiawang Xiong ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Class I ◽  
High Yield ◽  
Eating Quality ◽  
Cultivated Rice ◽  
Rice Varieties ◽  
Rice Quality ◽  
Appearance Quality ◽  
A Genome ◽  
Glutamine Amidotransferase

Abstract As a staple food for more than half of the world’s population, the importance of rice is self-evident. Compared with ordinary rice, rice cultivars with superior eating quality and appearance quality are more popular with consumers due to its unique taste and ornamental value, even if their price is much higher. Appearance quality and CEQ (cooking and eating quality) are two very important aspects in the evaluation of rice quality. Here, we performed a genome-wide association study on chalkiness rate in a diverse panel of 533 cultivated rice accessions. We identified a batch of potential chalky genes and prioritize one (LOC_Os03g48060) for functional analyses. Two floury outer endosperm mutants (flo19-1 and flo19-2) were generated through editing LOC_Os03g48060 (named as FLO19 in this study), which encodes a class I glutamine amidotransferase. The different performance of the two mutants in various storage substances directly led to completely different changes in CEQ. The mutation of FLO19 gene caused the damage of carbon and nitrogen metabolism in rice, which affected the normal growth and development of rice, including decreased plant height and yield loss by decreased grain filling rate. Through haplotype analysis, we identified a haplotype of FLO19 that can improve both CEQ and appearance quality of rice, Hap2, which provides a selection target for rice quality improvement, especially for high-yield indica rice varieties.

scholarly journals Physical and Milling Quality of Milled Rice in Indonesia

2021 ◽  
Vol 17 (2) ◽  
pp. 33-40
Author(s):  
Mahargono Kobarsih ◽  
Siti Dewi Indrasari
Keyword(s):  
High Yield ◽  
Eating Quality ◽  
Milled Rice ◽  
Rice Varieties ◽  
Rice Quality ◽  
Milling Quality ◽  
High Productivity ◽  
Pigmented Rice ◽  
Local Cultivar

More than 250 rice varieties are grown in Indonesia from new superior varieties and local varieties with aromatic, non-aromatic aromas and pigmented rice. Rice quality is one factor that must be considered in addition to high productivity. Generally, the quality of grain and rice quality in Indonesia have met the quality standards set based on SNI 0224-1987/SPI-TAN/01/01/1993 and SNI 6128:2020. Ricequality is determined by several factors such as grain appearance, nutritional value, cooking and eating quality and become one of the foremost considerations for rice buyers. Such information can be utilized as basic data of character of genetic resources on assembling of new superior varieties by rice breeders. Those information can be used as a descriptive information for farmers and rice productivity, high yield, and better rice quality. Good quality local cultivar can be used as parents for the formation of new superior varieties.

scholarly journals Response of Milling and Appearance Quality of Rice with Good Eating Quality to Temperature and Solar Radiation in Lower Reaches of Huai River

Agronomy ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 77
Author(s):  
Nianbing Zhou ◽  
Haiyan Wei ◽  
Hongcheng Zhang
Keyword(s):  
Solar Radiation ◽  
Field Experiments ◽  
Oryza Sativa L ◽  
National Standard ◽  
High Yield ◽  
Eating Quality ◽  
Rice Varieties ◽  
Appearance Quality ◽  
Huai River

The effects of temperature and solar radiation on milling and appearance quality of rice (Oryza sativa L.) were evaluated to find the optimal temperature and solar radiation for optimizing milling and appearance quality of rice in the lower reaches of Huai River. Field experiments were conducted with two medium-maturing japonica soft rice varieties (SMR), two late-maturing japonica soft rice varieties (SLR) and two late-maturing japonica non-soft rice varieties (LR) as experimental materials. Seeds were sown on 10 May (T1), 17 May (T2), 24 May (T3), 31 May (T4), 7 June (T5), 14 June (T6), and 21 June (T7) in 2017 and 2018. Compared with solar radiation, temperature was the main environmental factor affecting the milling and appearance quality of rice in the lower reaches of Huai River. Under the condition of ensuring relatively high-yield, the milling quality of SMR and SLR can reach the second grade of China’s national standard of high quality paddy. The mean daily temperature (Tmean) range were 20.2–22.7 °C and 20.4–22.0 °C respectively. The temperature range for LR to obtain a relatively high-yield, good milling and appearance quality was 20.4–20.7 °C. The optimal sowing dates of SMR, SLR and LR were 15 May to 1 June, 15 May to 20 May and 15 May to 20 May, respectively.

scholarly journals Genetic dissection of eating and cooking qualities in different subpopulations of cultivated rice (Oryza sativa L.) through association mapping

BMC Genetics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Chunfang Zhao ◽  
Ling Zhao ◽  
Qingyong Zhao ◽  
Tao Chen ◽  
Shu Yao ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Association Mapping ◽  
Genetic Factors ◽  
Amylose Content ◽  
Starch Synthesis ◽  
Cultivated Rice ◽  
Rice Varieties ◽  
Gene Markers ◽  
A Genome ◽  
Gel Consistency

Abstract Background Eating and cooking qualities (ECQs) of rice (Oryza sativa L.) determine consumer acceptance and the economic value of rice varieties. The starch physicochemical properties, i.e. amylose content, gel consistency, gelatinization temperature and pasting viscosity are important indices for evaluating rice ECQs. Genetic factors are required for development of rice varieties with excellent ECQs and association mapping is one of the promising approaches for discovering such associated genetic factors. Results A genome-wide association mapping was performed on a set of 253 non-glutinous rice accessions consisting of 83 indica and 170 japonica cultivated rice varieties through phenotyping for 11 ECQ traits in two consecutive years and genotyping with 210 polymorphic SSR and candidate-gene markers. These markers amplified 747 alleles with an average of 3.57 alleles per locus. The structure, phylogenetic relationship, and principal component analysis indicated a strong population differentiation between indica and japonica accessions and association mapping was thus undertaken within indica and japonica subpopulations. All traits showed a large phenotypic variation and highly significant phenotypic correlations were present between most of traits. A total of 33 and 30 loci were located for 11 ECQs in indica and japonica subpopulations respectively. Most of associated loci were overlapped with starch synthesis-related genes (SSRGs), and the Wx locus gathered 14 associated loci with the largest effects on amylose content, gel consistency and pasting viscosities. Eight subpopulation specific markers, RM588, Wx-(CT)n, SSI and SBE1 for indica subpopulation and RM550, Wxmp, SSIIa and SBE4 for japonica subpopulation, were identified, suggesting alleles of SSRGs showed the subspecific tendency. Nevertheless, allelic variation in SSIIa showed no tendency towards subspecies. One associated maker RM550 detected in japonica subpopulation for amylose content and pasting viscosity was verified a potential novel and stably expressed locus and could be selected for further fine mapping. Conclusion This study illustrated the potential for dissecting genetic factors of complex traits in domesticated rice subspecies and provided highly associated markers to facilitate marker-assisted selection for breeding high-quality indica or japonica rice varieties.

scholarly journals Identification of Gene Associated with Sweetness in Corn (Zea mays L.) by Genome-Wide Association Study (GWAS) and Development of a Functional SNP Marker for Predicting Sweet Corn

Plants ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 1239
Author(s):  
Vinitchan Ruanjaichon ◽  
Kanogporn Khammona ◽  
Burin Thunnom ◽  
Khundej Suriharn ◽  
Chalong Kerdsri ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Sweet Corn ◽  
Recombinant Inbred Lines ◽  
Snp Array ◽  
Genome Wide Association ◽  
Eating Quality ◽  
Quality Trait ◽  
Genome Wide ◽  
A Genome

Sweetness is an economically important eating quality trait for sweet-corn breeding. To investigate the genetic control of the sweetness trait, we conducted a genome-wide association study (GWAS) in an association panel consisting of 250 sweet corn and waxy corn inbred and recombinant inbred lines (RILs), together with the genotypes obtained from the high-density 600K maize genotyping single-nucleotide polymorphism (SNP) array. GWAS results identified 12 significantly associated SNPs on chromosomes 3, 4, 5, and 7. The most associated SNP, AX_91849634, was found on chromosome 3 with a highly significant p-value of ≤1.53 × 10−14. The candidate gene identified within the linkage disequilibrium (LD) of this marker was shrunken2 (Zm00001d044129; sh2), which encodes ADP-glucose pyrophosphorylase (AGPase), a 60 kDa subunit enzyme that affects starch metabolism in the maize endosperm. Several SNP markers specific to variants in sh2 were developed and validated. According to the validation in a set of 81 inbred, RIL, and popular corn varieties, marker Sh2_rs844805326, which was developed on the basis of the SNP at the position 154 of exon 1, was highly efficient in classifying sh2-based sweet corn from other types of corn. This functional marker is extremely useful for marker-assisted breeding in sh2-sweet corn improvement and marketable seed production.

scholarly journals Application of CRISPR/Cas9 Technology in the Genetic Improvement of Rice Yield and Quality Characters

2020 ◽  
Vol 11 (2) ◽  
pp. 62
Author(s):  
Bo Peng ◽  
Xiaorui Ma ◽  
Tao Yang ◽  
Mengyang Zheng ◽  
Juan Peng ◽  
...  
Keyword(s):  
Genetic Improvement ◽  
Rice Yield ◽  
Oryza Sativa L ◽  
High Yield ◽  
Rice Varieties ◽  
Continuous Increase ◽  
Rice Quality ◽  
Genome Region ◽  
New Genes ◽  
Yield And Quality

Rice (Oryza sativa L.) is one of the most important food crops in the world. With the continuous increase of global population and the continuous improvement of people's living standards, it has become the focus of attention of rice breeders and botanists to improve the yield and quality of rice. In the new genome editing technology, the CRISPR/Cas system can accurately and specifically edit the target genome region. In recent years, CRISPR/Cas9 technology has made important progress in studying the function of new genes, increasing rice yield and improving rice quality. Therefore, this paper mainly reviewed the application of CRISPR/Cas9 technology in the genetic improvement of rice yield and rice quality in recent years, and looked forward to the application prospect of CRISPR/Cas9 technology in rice genetic breeding, which will provide important reference for the cultivation of new high-quality and high-yield rice varieties.

scholarly journals A GWAS approach to find SNPs associated with salt removal in rice leaf sheath

2020 ◽  
Vol 126 (7) ◽  
pp. 1193-1202 ◽  
Author(s):  
Sarin Neang ◽  
Marjorie de Ocampo ◽  
James A Egdane ◽  
John Damien Platten ◽  
Abdelbagi M Ismail ◽  
...  
Keyword(s):  
Salt Stress ◽  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Significant Snps ◽  
Leaf Sheath ◽  
Salt Transport ◽  
Nucleotide Polymorphisms ◽  
Rice Varieties ◽  
Gwas Study ◽  
A Genome

Abstract Background and Aims The ability for salt removal at the leaf sheath level is considered to be one of the major mechanisms associated with salt tolerance in rice. Thus, understanding the genetic control of the salt removal capacity in leaf sheaths will help improve the molecular breeding of salt-tolerant rice varieties and speed up future varietal development to increase productivity in salt-affected areas. We report a genome-wide association study (GWAS) conducted to find single nucleotide polymorphisms (SNPs) associated with salt removal in leaf sheaths of rice. Methods In this study, 296 accessions of a rice (Oryza sativa) diversity panel were used to identify salt removal-related traits and conduct GWAS using 36 901 SNPs. The sheath:blade ratio of Na+ and Cl– concentrations was used to determine the salt removal ability in leaf sheaths. Candidate genes were further narrowed via Gene Ontology and RNA-seq analysis to those whose putative function was likely to be associated with salt transport and were up-regulated in response to salt stress. Key results For the association signals of the Na+ sheath:blade ratio, significant SNPs were found only in the indica sub-population on chromosome 5. Within candidate genes found in the GWAS study, five genes were upregulated and eight genes were downregulated in the internal leaf sheath tissues in the presence of salt stress. Conclusions These GWAS data imply that rice accessions in the indica variety group are the main source of genes and alleles associated with Na+ removal in leaf sheaths of rice under salt stress.

scholarly journals Integrating GWAS and Transcriptomics to Identify Genes Involved in Seed Dormancy in Rice

2021 ◽  
Author(s):  
Jin Shi ◽  
Jianxin Shi ◽  
Wanqi Liang ◽  
Dabing Zhang
Keyword(s):  
Candidate Genes ◽  
Seed Dormancy ◽  
Genome Wide Association Study ◽  
Crop Improvement ◽  
Heading Date ◽  
Differentially Expressed ◽  
Nucleotide Polymorphisms ◽  
Cultivated Rice ◽  
A Genome ◽  
Seed Harvest

Abstract Seed dormancy is a key agricultural trait to prevent pre-harvest sprouting in crop plants such as rice (Oryza sativa L.), wheat (Triticum aestivum), and barley (Hordeum vulgare L.). However, our knowledge of seed dormancy is hampered by the complexities of studying a trait that changes over time after seed harvest, and is complicated by interactions between phytohormones, other regulators, and the environment. Here, we have conducted a genome-wide association study using a panel of 311 natural accessions of cultivated rice, examining a total of 519,158 single nucleotide polymorphisms (SNPs). Eight quantitative trait loci (QTLs) were found to associate with seed dormancy; expression of candidate genes within 100 kb of each QTL was examined in two published, germination-specific transcriptomic datasets. Ten candidate genes, differentially expressed within the first four days post-imbibition, were identified. Five of these genes had previously been associated with awn length, heading date, yield, and spikelet length phenotypes. In addition, previously identified genes involved in hormone signaling during germination were found to be differentially expressed between a japonica and an indica line; SNPs in the promoter of Os9BGlu33 were associated with germination index. Collectively, our results are useful for future characterization of seed dormancy mechanism and crop improvement, and suggest haplotypes for further analysis that may be of use to boost PHS resistance in rice.

scholarly journals Combination of favorable gene haplotypes plays an important role in rice hybrid grain quality traits based on genome-wide association analysis

2020 ◽  
Author(s):  
Lanzhi Li ◽  
Xingfei Zheng ◽  
Xueli Zhang ◽  
Kai Xu ◽  
Shufeng Song ◽  
...  
Keyword(s):  
Grain Quality ◽  
Genome Wide Association Study ◽  
Amylose Content ◽  
Genome Wide Association ◽  
High Yield ◽  
Quality Trait ◽  
Rice Grain ◽  
Quality Traits ◽  
Genome Wide ◽  
A Genome

SummaryYield level and grain quality determine the commercial potential of rice (Oryza sativa L.) varieties. Mining and using genes that control important rice grain quality characteristics are major tasks for plant breeders. Here, a genome-wide association study was conducted to determine the genetic bases of 12 rice grain quality traits in 113 varieties and 565 testcross hybrids. A total of 56 significant SNPs were associated with 9 of the traits in variety phenotypic, general combining ability, testcross hybrid phenotypic and mid-parental heterotic datasets, from which 45 novel loci were identified. The cumulative effects of superior alleles or favorable haplotypes of genes closest to significant quality trait-associated loci were found in the four datasets. Additionally, the favorable gene haplotypes performed better than those of superior alleles in the variety and testcross hybrid datasets. Pyramiding the favorable haplotypes of five cloned rice grain quality genes resulted in a very low amylose content and high yield in the latter. These testcross hybrids had rice grain qualities similar to their parental lines but with much higher yields. The amylose content, grain width and grain length predictions for potential hybrids among the 113 varieties using genomic selection based on the BayesB method revealed a performance trend similar to those the testcross hybrids in our study. Thus, the selection of combination of favorable rice quality-related gene haplotypes is recommended to breed hybrids with high yields and elite grain qualities.

scholarly journals Tomato SD1, encoding a kinase-interacting protein, is a major locus controlling stem development

2020 ◽  
Vol 71 (12) ◽  
pp. 3575-3587
Author(s):  
Jie Ye ◽  
Ranwen Tian ◽  
Xiangfei Meng ◽  
Peiwen Tao ◽  
Changxing Li ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Fruit Size ◽  
Stem Diameter ◽  
Chromosome 9 ◽  
High Yield ◽  
Evolutionary Analysis ◽  
Long Distance ◽  
Interacting Protein ◽  
A Genome ◽  
Stem Development

Abstract Stems serve as key determinants of plant development by connecting and supporting parts of the plant body, transporting nutrients important for long-distance communication that affect crop yield, and producing new organs. Nonetheless, studies on the regulation of stem development in crops are rather limited. Here, we found a significant correlation (P<0.001) between stem diameter (SD) and fruit size in tomato (Solanum lycopersicum). We performed a genome-wide association study and identified a novel quantitative trait locus (QTL), SDR9 (stem diameter regulator on CHROMOSOME 9), that co-localized with a gene encoding a kinase-interacting family protein (KIP), which is the most likely candidate gene related to SD (hereafter referred to as SD1). Overexpression of SD1 in thin-stem accessions resulted in increased SD. In contrast, suppressed expression of SD1 in thick-stem accessions using RNA interference exhibited the opposite effect. Further microscopic analyses showed that SD1 affected the stem diameter by controlling the size and number of secondary phloem cells. An 11-bp indel in the promoter region of SD1 that disrupts a gibberellin-responsive cis-element was linked to SD. Expression analysis revealed that SD1 was mainly expressed at the cambium of the stem and positively regulates stem development. Evolutionary analysis revealed that the thick-stem allele of SD1 was selected during the recent process of tomato improvement. Our results provide novel genetic and molecular insight into natural variation of SD in tomato and may accelerate the breeding of high yield tomato.

scholarly journals Candidate Gene Analysis for Nitrogen Absorption and Utilization in Japonica Rice at the Seedling Stage Based on a Genome-Wide Association Study

2021 ◽  
Vol 12 ◽  
Author(s):  
Wei Xin ◽  
Jingguo Wang ◽  
Jia Li ◽  
Hongwei Zhao ◽  
Hualong Liu ◽  
...  
Keyword(s):  
Grain Yield ◽  
Association Study ◽  
Candidate Gene ◽  
Genome Wide Association Study ◽  
Negative Impact ◽  
Genome Wide Association ◽  
Japonica Rice ◽  
Rice Varieties ◽  
Genome Wide ◽  
A Genome

Over-application of nitrogen (N) fertilizer in fields has had a negative impact on both environment and human health. Domesticated rice varieties with high N use efficiency (NUE) reduce fertilizer requirements, enabling sustainable agriculture. Genome-wide association study (GWAS) analysis of N absorption and utilization traits under low and high N conditions was performed to obtain 12 quantitative trait loci (QTLs) based on genotypic data including 151,202 single-nucleotide polymorphisms (SNPs) developed by re-sequencing 267 japonica rice varieties. Eighteen candidate genes were obtained by integrating GWAS and transcriptome analyses; among them, the functions of OsNRT2.4, OsAMT1.2, and OsAlaAT genes in N transport and assimilation have been identified, and OsJAZ12 and OsJAZ13 also play important roles in rice adaptation to abiotic stresses. A NUE-related candidate gene, OsNAC68, was identified by quantitative real-time PCR (qRT-PCR) analyses. OsNAC68 encodes a NAC transcription factor and has been shown to be a positive regulator of the drought stress response in rice. Overexpression of OsNAC68 significantly increased rice NUE and grain yield under deficient N conditions, but the difference was not significant under sufficient N conditions. NUE and grain yield significantly decreased under both N supply conditions in the osbnac68 mutant. This study provides crucial insights into the genetic basis of N absorption and utilization in rice, and a NUE-related gene, OsNAC68, was cloned to provide important resources for rice breeding with high NUE and grain yield.

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