GRAIN LENGTH AND AWN 1 negatively regulates grain size in rice

Grain size is a key factor influencing the grain yield in rice. To identify the as-yet-unknown genes regulating grain size in Korean japonica rice, we developed a recombinant inbred line population (n = 162) from a cross between Odae (large-grain) and Joun (small-grain), and measured six traits including the thousand-grain weights of unhulled and hulled seeds, grain area, grain length, grain width and grain length-to-width ratio using high-throughput image analysis at the F8 and F9 generations. A genetic map was constructed using 248 kompetitive allele-specific PCR (KASP) markers that were polymorphic between the parental genotypes, and 29 QTLs affecting the six traits were identified, of which 15 were stable in both F8 and F9 generations. Notably, three QTL clusters affecting multiple traits were detected on chromosomes 6, 7 and 11. We analyzed whole-genome resequencing data of Odae and Joun, and selected candidate genes for the stable QTLs in the identified clusters that have high- or moderate-impact variations between Odae and Joun and encode proteins the families of which have been reported to be related to grain size regulation. These results will facilitate the identification of genes underlying the QTLs and promote molecular breeding of high-yielding Korean japonica rice varieties.

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CRISPR/Cas9 Guided Mutagenesis of Grain Size 3 Confers Increased Rice (Oryza sativa L.) Grain Length by Regulating Cysteine Proteinase Inhibitor and Ubiquitin-Related Proteins

International Journal of Molecular Sciences ◽

10.3390/ijms22063225 ◽

2021 ◽

Vol 22 (6) ◽

pp. 3225

Author(s):

Babar Usman ◽

Neng Zhao ◽

Gul Nawaz ◽

Baoxiang Qin ◽

Fang Liu ◽

...

Keyword(s):

Grain Size ◽

Proteinase Inhibitor ◽

Cysteine Proteinase ◽

Differentially Expressed ◽

Pathway Enrichment Analysis ◽

Cysteine Proteinase Inhibitor ◽

Rice Transformation ◽

Cysteine Synthase ◽

Grain Length ◽

Vacuolar Protein

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated protein (Cas9)-mediated genome editing has become an important way for molecular breeding in crop plants. To promote rice breeding, we edited the Grain Size 3 (GS3) gene for obtaining valuable and stable long-grain rice mutants. Furthermore, isobaric tags for the relative and absolute quantitation (iTRAQ)-based proteomic method were applied to determine the proteome-wide changes in the GS3 mutants compared with wild type (WT). Two target sites were designed to construct the vector, and the Agrobacterium-mediated method was used for rice transformation. Specific mutations were successfully introduced, and the grain length (GL) and 1000-grain weight (GWT) of the mutants were increased by 31.39% and 27.15%, respectively, compared with WT. The iTRAQ-based proteomic analysis revealed that a total of 31 proteins were differentially expressed in the GS3 mutants, including 20 up-regulated and 11 down-regulated proteins. Results showed that differentially expressed proteins (DEPs) were mainly related to cysteine synthase, cysteine proteinase inhibitor, vacuolar protein sorting-associated, ubiquitin, and DNA ligase. Furthermore, functional analysis revealed that DEPs were mostly enriched in cellular process, metabolic process, binding, transmembrane, structural, and catalytic activities. Pathway enrichment analysis revealed that DEPs were mainly involved in lipid metabolism and oxylipin biosynthesis. The protein-to-protein interaction (PPI) network found that proteins related to DNA damage-binding, ubiquitin-40S ribosomal, and cysteine proteinase inhibitor showed a higher degree of interaction. The homozygous mutant lines featured by stable inheritance and long-grain phenotype were obtained using the CRISPR/Cas9 system. This study provides a convenient and effective way of improving grain yield, which could significantly accelerate the breeding process of long-grain japonica parents and promote the development of high-yielding rice.

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GWAS identifies a wheat orthologue of the rice D11 gene as an important contributor to grain size in an international collection of hexaploid wheat

10.21203/rs.3.rs-244194/v1 ◽

2021 ◽

Author(s):

Honoré Tekeu ◽

Eddy L.M. Ngonkeu ◽

Sébastien Bélanger ◽

Pierre F. Djocgoué ◽

Amina Abed ◽

...

Keyword(s):

Grain Size ◽

Hexaploid Wheat ◽

Snp Array ◽

Genotyping By Sequencing ◽

Snp Markers ◽

Promising Candidate ◽

Single Nucleotide ◽

Grain Length ◽

Snp Data ◽

Genomic Regions

Abstract Grain size is a key agronomic trait that contributes to grain yield in hexaploid wheat. Grain length and width were evaluated in an international collection of 159 wheat accessions. These accessions were genetically characterized using a genotyping-by-sequencing (GBS) protocol that produced 73,784 single nucleotide polymorphism (SNP) markers. GBS-derived genotype calls obtained on Chinese Spring proved extremely accurate when compared to the reference (> 99.9%) and showed > 95% agreement with calls made at SNP loci shared with the 90K SNP array on a subset of 71 Canadian wheat accessions for which both types of data were available. This indicates that GBS can yield a large amount of highly accurate SNP data in hexaploid wheat. The genetic diversity analysis performed using this set of SNP markers revealed the presence of six distinct groups within this collection. A GWAS was conducted to uncover genomic regions controlling variation for grain length and width. In total, seven SNPs were found to be associated with one or both traits, identifying three quantitative trait loci (QTLs) located on chromosomes 1D, 2D and 4A. In the vicinity of the peak SNP on chromosome 2D, we found a promising candidate gene (TraesCS2D01G331100), whose rice ortholog (D11) had previously been reported to be involved in the regulation of grain size. These markers will be useful in breeding for enhanced wheat productivity.

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An Adenylate Kinase OsAK3 Involves Brassinosteroid Signaling and Grain Length in Rice (Oryza sativa L.)

Rice ◽

10.1186/s12284-021-00546-0 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Jiaqi Zhang ◽

Xiuying Gao ◽

Guang Cai ◽

Yuji Wang ◽

Jianbo Li ◽

...

Keyword(s):

Grain Size ◽

Adenylate Kinase ◽

Oryza Sativa L ◽

Transcriptional Level ◽

Grain Length ◽

Brassinosteroid Signaling ◽

Dna Insertion ◽

Coleoptile Elongation

Abstract Background Grain size is one of the major determinants of cereal crop yield. As a class of plant polyhydroxysteroids, brassinosteroids (BRs) play essential roles in the regulation of grain size and plant architecture in rice. In a previous research, we cloned qGL3/OsPPKL1 encoding a protein phosphatase with Kelch-like repeat domains, which negatively regulates BR signaling and grain length in rice. Results Here, we screened qGL3-interacting proteins (GIPs) via yeast two-hybrid assay and analyzed the phenotypes of the T-DNA insertion mutants of GIPs. Among these mutants, mutant osak3 presents shorter grain length and dwarfing phenotype. OsAK3 encodes an adenylate kinase, which regulates grain size by controlling cell expansion of rice spikelet glume. Overexpression of OsAK3 resulted in longer grain length. OsAK3 interacts with qGL3 in vivo and in vitro. Lamina inclination, coleoptile elongation and root inhibition experiments showed that the osak3 mutant was less sensitive to exogenous brassinolide (BL) treatment. The transcriptional level of OsAK3 was up-regulated under BL induction. In addition, RNA-Seq data indicate that OsAK3 is involved in a variety of biological processes that regulate BR signaling and grain development in rice. Conclusions Our study reveals a novel BR signaling component OsAK3 in the regulation of grain length, and provides novel clues for uncovering the potential functions of OsAK3 in rice growth and development.

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Validation of a QTL for Grain Size and Weight Using an Introgression Line from a Cross between Oryza sativa and Oryza minuta

Rice ◽

10.1186/s12284-021-00472-1 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Yue Feng ◽

Xiaoping Yuan ◽

Yiping Wang ◽

Yaolong Yang ◽

Mengchen Zhang ◽

...

Keyword(s):

Grain Size ◽

Oryza Sativa ◽

Candidate Genes ◽

Introgression Line ◽

Grain Weight ◽

Chromosome 7 ◽

Thousand Grain Weight ◽

Grain Length ◽

Oryza Minuta ◽

Grain Width

Abstract Background Grain size and weight are important target traits determining grain yield and quality in rice. Wild rice species possess substantial elite genes that can be served as an important resource for genetic improvement of rice. In this study, we identify and validate a novel QTL on chromosome 7 affecting the grain size and weight using introgression lines from cross of Oryza sativa and Oryza minuta. Results An introgression line ‘IL188’ has been achieved from a wild species Oryza minuta (2n = 48, BBCC, W303) into O. sativa japonica Nipponbare. The F2 and F2:3 populations derived from a cross between IL188 and Nipponbare were used to map QTLs for five grain size traits, including grain length (GL), grain width (GW), grain length to width ratio (LWR), grain thickness (GT) and thousand grain weight (TGW). A total of 12 QTLs for the five grain traits were identified on chromosomes 1, 2, 3, 6, 7, and 8. The QTL-qGL7 controlling GL on chromosome 7 was detected stably in the F2 and F2:3 populations, and explained 15.09–16.30% of the phenotypic variance. To validate the effect of qGL7, eight residual heterozygous line (RHL) populations were developed through selfing four F2:3 and four F2:4 plants with different heterozygous segments for the target region. By further developing SSR and Indel markers in the target interval, qGL7 was delimited to a ~ 261 kb region between Indel marker Y7–12 and SSR marker Y7–38, which also showed significant effects on grain width and thousand grain weight. Comparing with the reference genome of Nipponbare, stop or frameshift mutations in the exon of the three putative genes LOC_Os07g36830, LOC_Os07g36900 and LOC_Os07g36910 encoding F-box domain-containing proteins may be the candidate genes for qGL7. Scanning electron microscopy analysis of the glume’s epidermal cells showed that the cell length and width of NIL-qGL7IL188 was higher than NIL-qGL7Nip, indicating that qGL7 increases grain size and weight by regulating cell expansion. Conclusions In this study, we detected 12 QTLs regulating grain size and weight using an introgression line from a cross between Oryza sativa and Oryza minuta. Of these loci, we confirmed and delimited the qGL7 to a ~ 261 kb region. Three putative genes, LOC_Os07g36830, LOC_Os07g36900 and LOC_Os07g36910 encoding F-box domain-containing proteins may be the candidate genes for qGL7. These results provide a basis for map-based cloning of the qGL7 gene and useful information for marker assisted selection in rice grain quality improvement.

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GWAS identifies an ortholog of the rice D11 gene as a candidate gene for grain size in an international collection of hexaploid wheat

Scientific Reports ◽

10.1038/s41598-021-98626-0 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Honoré Tekeu ◽

Eddy L. M. Ngonkeu ◽

Sébastien Bélanger ◽

Pierre F. Djocgoué ◽

Amina Abed ◽

...

Keyword(s):

Grain Size ◽

Candidate Gene ◽

Hexaploid Wheat ◽

Snp Array ◽

Genotyping By Sequencing ◽

Snp Markers ◽

Single Nucleotide ◽

Grain Length ◽

Snp Data ◽

Genomic Regions

AbstractGrain size is a key agronomic trait that contributes to grain yield in hexaploid wheat. Grain length and width were evaluated in an international collection of 157 wheat accessions. These accessions were genetically characterized using a genotyping-by-sequencing (GBS) protocol that produced 73,784 single nucleotide polymorphism (SNP) markers. GBS-derived genotype calls obtained on Chinese Spring proved extremely accurate when compared to the reference (> 99.9%) and showed > 95% agreement with calls made at SNP loci shared with the 90 K SNP array on a subset of 71 Canadian wheat accessions for which both types of data were available. This indicates that GBS can yield a large amount of highly accurate SNP data in hexaploid wheat. The genetic diversity analysis performed using this set of SNP markers revealed the presence of six distinct groups within this collection. A GWAS was conducted to uncover genomic regions controlling variation for grain length and width. In total, seven SNPs were found to be associated with one or both traits, identifying three quantitative trait loci (QTLs) located on chromosomes 1D, 2D and 4A. In the vicinity of the peak SNP on chromosome 2D, we found a promising candidate gene (TraesCS2D01G331100), whose rice ortholog (D11) had previously been reported to be involved in the regulation of grain size. These markers will be useful in breeding for enhanced wheat productivity.

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Small grain screenings in wheat—using the grain size distribution for predicting cultivar responses

Australian Journal of Agricultural Research ◽

10.1071/ar05272 ◽

2006 ◽

Vol 57 (7) ◽

pp. 771 ◽

Cited By ~ 3

Author(s):

D. L. Sharma ◽

M. F. D'Antuono ◽

W. K. Anderson

Keyword(s):

Grain Size ◽

Size Distribution ◽

Grain Size Distribution ◽

Laplace Distribution ◽

Grain Weight ◽

Average Weight ◽

Grain Length ◽

Breeding Material ◽

Small Width ◽

Flour Yield

Small grain is a concern for wheat growers in water-limited environments worldwide. Following from our preliminary results that cultivars can differ for small grain screenings despite similarity of average grain weight in wheat, grain size distribution was investigated with the aim of identifying alternative parameters that could more reliably discriminate cultivars for their tendency to screenings without actually subjecting breeding material to harsh environments. Pre-cleaned harvest samples (using screen with 1.5-mm-wide holes) of 5 cultivars from 2 field cultivar × time of sowing experiments were divided into 5 grain-width fractions using 4 sieves with holes from 2.5 to 3.4-mm wide. The experiments conducted in the Western Australian wheatbelt experienced a dry finish in 2000 and a relatively wetter year in 2003. The grain that was separated into each width fraction was weighed and the average weight of grains for each fraction (called the size-specific weight) was derived from a subsample. The weight of grain (expressed as a percentage of the whole) collected between the 2.8 and 3.1-mm screens (fraction F3) was highly and negatively correlated with small grain screenings (r = –0.85; P < 0.001), thus strengthening the perception that screenings percentages may follow a certain form of grain size distribution. Among various grain size distributions, the skew-Laplace distribution fitted on grain weight was found to be the most suitable to characterise the cultivars. This provides a general approach in the examination of a grain size distribution, which is invariant to combinations of sieve sizes that different individuals may choose. We conclude that: (i) parameters µ and 1/α of the skew-Laplace distribution based on grain weight separated into each fraction can be used as a selection tool in predicting propensity for small grain screenings in wheat without having to subject breeding material to harsh conditions; (ii) higher values for both µ and 1/α are desirable but if the cultivar has small µ, a high 1/α is required to reduce screenings; (iii) breeders could consider the grain size distribution in addition to grain weight as a breeding objective; and (iv) millers should be looking for higher average grain weight and higher weight per unit grain length especially at small width fractions, to maximise flour yield. Hence, we anticipate that future research into aspects of starch packaging such as grain shape and endosperm density will optimise grain size distribution, grain weight per unit grain length, and eventually the flour yield per unit land area.

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Analysis of QTL for Grain Size in a Rice Chromosome Segment Substitution Line Z1392 with Long Grains and Fine Mapping of qGL-6

Rice ◽

10.1186/s12284-020-00399-z ◽

2020 ◽

Vol 13 (1) ◽

Author(s):

Ting Zhang ◽

Shiming Wang ◽

Shuangfei Sun ◽

Yi Zhang ◽

Juan Li ◽

...

Keyword(s):

Grain Size ◽

Epistatic Interaction ◽

Rice Chromosome ◽

Substitution Line ◽

Chromosome 6 ◽

Chromosome Segment Substitution Line ◽

Substitution Lines ◽

Grain Length ◽

Single Segment Substitution Lines ◽

Segment Substitution

Abstract Background Grain size affects not only rice yield but is also an important element in quality of appearance. However, the mechanism for inheritance of grain size is unclear. Results A rice chromosome segment substitution line Z1392, which harbors three substitution segments and produces grains of increased length, was identified. The three chromosome segments were located on chromosomes 1, 5, and 6, and the average length of the substitution segment was 3.17 Mb. Cytological analysis indicates that the predominant cause of increased grain length in Z1392 could be cell expansion in the glumes. Seven quantitative trait loci (QTLs) for grain size related traits were identified using the secondary F2 population produced by Nipponbare/Z1392. The inheritance of grain length in Z1392 was mainly controlled by two major QTLs, qGL-5 and qGL-6. qGL-6 was localized on a 1.26 Mb region on chromosome 6, and OsARF19 may be its candidate gene. Based on QTL mapping, three single-segment substitution lines (S1, S2, and S3) and two double-segment substitution lines (D1 and D2) were selected, and the mapping accuracy for qGL-5 and qGL-6 was further verified using three single-segment substitution lines. Analysis of QTL additive and epistatic effects revealed that the additive effect of alleles qGL-5 and qGL-6 from ‘Xihui 18’ was estimated to increase grain length of Z1392 by 0.22 and 0.15 mm, respectively. In addition, a positive epistatic interaction between qGL-5 and qGL-6 was detected, which indicates that the pyramiding of qGL-5 and qGL-6 for grain length produces a novel genotype with longer grains. Conclusions Inheritance of grain length in the triple-segment substitution line Z1392 is mainly controlled by two major QTLs, qGL-5 and qGL-6. qGL-6 was found to be located in a 1.26 Mb region on chromosome 6, and OsARF19 may be its candidate gene. A positive epistatic interaction between qGL-5 and qGL-6 results in longer grains. The present results can be used to facilitate cloning of the qGL-5 and qGL-6 genes and contribute to improvement of grain yield in rice.

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Characterization of Functional Genes GS3 and GW2 and their Effect on the Grain Size of Various Landraces of Rice

10.21203/rs.3.rs-1024333/v1 ◽

2021 ◽

Author(s):

Haroon Rasheed ◽

Sajid Fiaz ◽

Muhammad Abid Khan ◽

Sultan Mehmood ◽

Faizan Ullah ◽

...

Keyword(s):

Grain Size ◽

Grain Weight ◽

Negative Regulator ◽

Yield Potential ◽

Phenotypic Traits ◽

Dominant Allele ◽

Diverse Range ◽

Grain Length ◽

Grain Width ◽

1000 Grain Weight

Abstract Grain size is an essential factor in grain quality and yield. In the existing agricultural lands in Pakistan and even all over the world, genetics in rice works better for yield potential and quality improvement. GS3 and GW2 with functional mutation responsible for grain size in rice. In the current study, 17 different Pakistani landraces of various genetic and geographic backgrounds were evaluated for grain phenotypic traits (thousand-grain weight, length, width, and thickness) and characterized genotypes for GS3 gene (grain length) and GW2 (grain width). The two accessions JP5 and Bas370, were used as control. Phenotypic data revealed the range for grain weight from 16.86g (Lateefy) to 26.91g (PS2), grain length ranged from 7.27 mm (JP-5) to 12.18 mm (PS2), grain width ranged from 2.01 mm (Lateefy) to 3.51 mm (JP5), and grain thickness ranged from 1.79 mm to 2.19. Pearson correlation revealed a negative and significant correlation between grain width and length. There was no significant correlation between grain length and 1000-grain weight and grain width. LSD test displayed that the means of three variables grain length, grain width, and 1000-grain weight were statistically different from one another except grain width and grain breadth. GS3 is a negative regulator of grain length. Fifteen accessions GA-5015, PS-2, Swat-1, Swat-2, DR-2, Dilrosh, Malhar-346, Kashmir Basmati, Rachna Basmati, KS-282, Basmati-370, KSK-133, KSK-434, MG-Basmati, and Lateefy, carried the domesticated allele of GS3 while JP5 and Fakhr-e-Malakand carried the dominant allele. Similarly, the GW2 is a negative regulator of grain width. Fifteen accessions, i.e., Bas-370, GA-5015, PS-2, Swat-1, Swat-2, DR-2, Dilrosh, Malhar-346, Kashmir Basmati, Rachna Basmati, KS-282, KSK-133, KSK-434, MG-Basmati, and Lateefy carried the dominant allele while JP-5 and Fakhr-e-Malakand carried the mutant allele. The current phenotypic evaluation of the Germplasm revealed a diverse range of grain size of Pakistani landraces and also suggests that the selection of grain length in Pakistani landraces was independent of 1000-grain weight. The accessions with genotypic characterization will aid in marker-assisted breeding programs to break the stagnant yield prevail for the last few decades in Pakistan.

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Validation of a QTL for grain size and weight using an introgression line from a cross between Oryza sativa and Oryza minuta

10.21203/rs.3.rs-54218/v2 ◽

2021 ◽

Author(s):

Yue Feng ◽

Xiaoping Yuan ◽

Yiping Wang ◽

Yaolong Yang ◽

Mengchen Zhang ◽

...

Keyword(s):

Grain Size ◽

Oryza Sativa ◽

Candidate Genes ◽

Introgression Line ◽

Grain Weight ◽

Chromosome 7 ◽

Thousand Grain Weight ◽

Grain Length ◽

Oryza Minuta ◽

Grain Width

Abstract Background: Grain size and weight are important target traits determining grain yield and quality in rice. Wild rice species possess substantial elite genes that can be served as an important resource for genetic improvement of rice. In this study, we identify and validate a novel QTL on chromosome 7 affecting the grain size and weight using introgression lines from cross of Oryza sativa and Oryza minuta. Results: An introgression line ‘IL188’ has been achieved from a wild species Oryza minuta (2n = 48, BBCC, W303) into O. sativa japonica Nipponbare. The F2 and F2:3 populations derived from a cross between IL188 and Nipponbare were used to map QTLs for five grain size traits, including grain length (GL), grain width (GW), grain length to width ratio (LWR), grain thickness (GT) and thousand grain weight (TGW). A total of 12 QTLs for the five grain traits were identified on chromosomes 1, 2, 3, 6, 7, and 8. The QTL-qGL7 controlling GL on chromosome 7 was detected stably in the F2 and F2:3 populations, and explained 15.09-16.30% of the phenotypic variance. To validate the effect of qGL7, eight residual heterozygous line (RHL) populations were developed through selfing four F2:3 and four F2:4 plants with different heterozygous segments for the target region. By further developing SSR and Indel markers in the target interval, qGL7 was delimited to a ~261 kb region between Indel marker Y7-12 and SSR marker Y7-38, which also showed significant effects on grain width and thousand grain weight. Comparing with the reference genome of Nipponbare, stop or frameshift mutations in the exon of the three putative genes LOC_Os07g36830, LOC_Os07g36900 and LOC_Os07g36910 encoding F-box domain-containing proteins may be the candidate genes for qGL7. Scanning electron microscopy analysis of the glume's epidermal cells showed that the cell length and width of NIL-qGL7IL188 was higher than NIL-qGL7Nip, indicating that qGL7 increases grain size and weight by regulating cell expansion. Conclusions: In this study, we detected 12 QTLs regulating grain size and weight using an introgression line from a cross between an Oryza sativa and Oryza minuta. Of these loci, we confirmed and delimited the qGL7 to a ~261 kb region. Three putative genes, LOC_Os07g36830, LOC_Os07g36900 and LOC_Os07g36910 encoding F-box domain-containing proteins may be the candidate genes for qGL7. These results provide a basis for map-based cloning of the qGL7 gene and useful information for marker assisted selection in rice grain quality improvement.

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