Dissection of Closely Linked QTLs Controlling Grain Size in Rice

Abstract Grain size is a key constituent of grain weight and appearance in rice. However, insufficient attention has been paid to the small-effect QTLs on grain size. In the present study, residual heterozygous populations were developed for mapping two genetically linked small-effect QTLs for grain size. After genotyping and phenotyping of five successive generations, qGS7.1 was dissected into three QTLs and two were selected for further analysis. qTGW7.2a was finally mapped into a 21.10-kb interval containing four annotated candidate genes. Transcript levels assay showed that the expression of candidates LOC_Os07g39490 and LOC_Os07g39500 were significantly reduced in the NIL- qTGW7.2a BG1 . Cytological observation indicated that qTGW7.2a regulated grain width through controlling cell expansion. Use the same strategy, qTGW7.2b was fine mapped into a 52.71-kb interval, showing a significant effect on grain length and width with opposite allelic directions but little on grain weight. Our study provides new genetic resources for yield improvement and fine-tunes of grain size in rice.

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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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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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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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Characterization of Potential Candidate Genes for Grain Size in Wild Emmer Wheat Triticum Dicoccoides

10.21203/rs.3.rs-705356/v1 ◽

2021 ◽

Author(s):

Sanket Shinde ◽

Guriqbal Singh Dhillon ◽

Amandeep Kaur ◽

Parveen Chhuneja ◽

Achla Sharma ◽

...

Keyword(s):

Grain Size ◽

Candidate Genes ◽

Triticum Dicoccoides ◽

Grain Weight ◽

Potential Candidate ◽

Grain Length ◽

Study Gene Expression ◽

Component Traits ◽

Wheat Wild Relatives

Abstract There is an incessant need to address food security in staple crops, and the crop yield is positively correlated with grain weight. Grain size, determined by grain length and width, is an essential component of final grain weight in cereals. Wheat wild relatives are the goldmine to harness any trait of interest, including the component traits of grain size. It is crucial to understand the detailed mechanism of grain size formation and unravel underlying genes controlling grain size in these species for their proper utilization in wheat improvement. In this study, gene expression analysis was performed on developing grain in wild tetraploid progenitor Triticum dicoccoides (AABB) to identify candidate genes involved in determining grain size. Four T. dicoccoides accessions were selected, two (pau5228 and pau5322) with higher grain length and weight and two (pau14703 and pau14756) with comparatively smaller grains.Six genes out of the eight genes selected for expression study, viz., GL7, TaGL3, TaGS5, GS3, SRS3, and TaGASR7, were upregulated from 8 days post-anthesis (DPA) to 20 DPA in both the large grain accessions, while TaGW2 gene was upregulated in both small grain accessions. TGW6 was downregulated in all the accessions at all stages of grain development. The results indicated that the selected genes play an essential role in grain size formation by controlling individual morphometric components of grain length and width. Targeted introgression genes controlling grain size components will eventually aid in improving grains yield.

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Influence of heterosis value in spring wheat hybrids on the efficiency of valuable selection

сборник статей всероссийской научной конференции с международным участием "Растениеводство и луговодство" ◽

10.26897/978-5-9675-1762-4-2020-78 ◽

2020 ◽

Author(s):

A. G. Abramov ◽

◽

I.N. Abramova

Keyword(s):

Grain Size ◽

Spring Wheat ◽

Grain Weight ◽

Irkutsk Region ◽

Wheat Hybrids

The article presents the results of the influence of the magnitude of heterosis on the main elements of the formation of yield (grain size and productivity of the main spike) of spring wheat in the Irkutsk region. The following were used as maternal varieties: Irgina, Krasnoyarskaya 83, Tulun 15, Tselinnaya 60, Altayskaya 92, Niva 2 and a variety from Mongolia Orkhon 85, as testers - Skala, Angara 86, Tulunskaya 12 The best indicators of hypothetical heterosis were manifested by the number of grains in ear in combinations Krasnoyarskaya 83 × Angara 86, Krasnoyarskaya 83 × Skala, Altai 92 × Skala (81.6 ... 85.7%). In terms of grain weight from the main spike, the best results of hypothetical heterosis were noted in hybrid combinations Krasnoyarskaya 83 × Angara 86, Orkhon 85 × Angara 86, Ni-va × Angara 86, Altai 92 × Angara 86 (100.0 ... 130.7%) ... Krasnoyarskaya 83 × Angara 86, Altai 92 × Angara 86, Or-khon × Angara 86 are recognized as the best hybrid combinations that can give the greatest yield of transgressive forms of elite plants.

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Genome-wide association study and gene network analyses reveal potential candidate genes for high night temperature tolerance in rice

Scientific Reports ◽

10.1038/s41598-021-85921-z ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Raju Bheemanahalli ◽

Montana Knight ◽

Cherryl Quinones ◽

Colleen J. Doherty ◽

S. V. Krishna Jagadish

Keyword(s):

Grain Size ◽

Candidate Genes ◽

Gene Network ◽

Genome Wide Association ◽

Potential Candidate ◽

Genetic Loci ◽

Stay Green ◽

Yield And Quality ◽

Genome Wide ◽

Wide Range

AbstractHigh night temperatures (HNT) are shown to significantly reduce rice (Oryza sativa L.) yield and quality. A better understanding of the genetic architecture of HNT tolerance will help rice breeders to develop varieties adapted to future warmer climates. In this study, a diverse indica rice panel displayed a wide range of phenotypic variability in yield and quality traits under control night (24 °C) and higher night (29 °C) temperatures. Genome-wide association analysis revealed 38 genetic loci associated across treatments (18 for control and 20 for HNT). Nineteen loci were detected with the relative changes in the traits between control and HNT. Positive phenotypic correlations and co-located genetic loci with previously cloned grain size genes revealed common genetic regulation between control and HNT, particularly grain size. Network-based predictive models prioritized 20 causal genes at the genetic loci based on known gene/s expression under HNT in rice. Our study provides important insights for future candidate gene validation and molecular marker development to enhance HNT tolerance in rice. Integrated physiological, genomic, and gene network-informed approaches indicate that the candidate genes for stay-green trait may be relevant to minimizing HNT-induced yield and quality losses during grain filling in rice by optimizing source-sink relationships.

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Grain Size Selection Using Novel Functional Markers Targeting 14 Genes in Rice

Rice ◽

10.1186/s12284-020-00427-y ◽

2020 ◽

Vol 13 (1) ◽

Author(s):

Lin Zhang ◽

Bin Ma ◽

Zhong Bian ◽

Xiaoyuan Li ◽

Changquan Zhang ◽

...

Keyword(s):

Grain Size ◽

Grain Yield ◽

Rational Design ◽

Width Ratio ◽

Functional Markers ◽

Rice Breeding ◽

Nucleotide Polymorphisms ◽

Yield And Quality ◽

Grain Width ◽

Grain Yield And Quality

Abstract Background Grain size is an extremely important aspect of rice breeding, affecting both grain yield and quality traits. It is controlled by multiple genes and tracking these genes in breeding schemes should expedite selection of lines with superior grain yield and quality, thus it is essential to develop robust, efficient markers. Result In this study, 14 genes related to grain size (GW2, GS2, qLGY3, GS3, GL3.1, TGW3, GS5, GW5, GS6, TGW6, GW6a, GLW7, GL7 and GW8) were selected for functional marker development. Twenty-one PCR-gel-based markers were developed to genotype the candidate functional nucleotide polymorphisms (FNPs) of these genes, and all markers can effectively recognize the corresponding allele types. To test the allele effects of different FNPs, a global collection of rice cultivars including 257 accessions from the Rice Diversity Panel 1 was used for allele mining, and four grain-size-related traits were investigated at two planting locations. Three FNPs for GW2, GS2 and GL3.1 were genotyped as rare alleles only found in cultivars with notably large grains, and the allele contributions of the remaining FNPs were clarified in both the indica and japonica subspecies. Significant trait contributions were found for most of the FNPs, especially GS3, GW5 and GL7. Of note, GW5 could function as a key regulator to coordinate the performance of other grain size genes. The allele effects of several FNPs were also tested by QTL analysis using an F2 population, and GW5 was further identified as the major locus with the largest contribution to grain width and length to width ratio. Conclusions The functional markers are robust for genotyping different cultivars and may facilitate the rational design of grain size to achieve a balance between grain yield and quality in future rice breeding efforts.

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The Rho-family GTPase OsRac1 controls rice grain size and yield by regulating cell division

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1902321116 ◽

2019 ◽

Vol 116 (32) ◽

pp. 16121-16126 ◽

Cited By ~ 5

Author(s):

Ying Zhang ◽

Yan Xiong ◽

Renyi Liu ◽

Hong-Wei Xue ◽

Zhenbiao Yang

Keyword(s):

Grain Size ◽

Cell Division ◽

Grain Yield ◽

Molecular Mechanisms ◽

Grain Filling ◽

High Yield ◽

Rice Grain ◽

Rop Gtpase ◽

Key Factor ◽

Grain Width

Grain size is a key factor for determining grain yield in crops and is a target trait for both domestication and breeding, yet the mechanisms underlying the regulation of grain size are largely unclear. Here we show that the grain size and yield of rice (Oryza sativa) is positively regulated by ROP GTPase (Rho-like GTPase from plants), a versatile molecular switch modulating plant growth, development, and responses to the environment. Overexpression of rice OsRac1ROP not only increases cell numbers, resulting in a larger spikelet hull, but also accelerates grain filling rate, causing greater grain width and weight. As a result, OsRac1 overexpression improves grain yield in O. sativa by nearly 16%. In contrast, down-regulation or deletion of OsRac1 causes the opposite effects. RNA-seq and cell cycle analyses suggest that OsRac1 promotes cell division. Interestingly, OsRac1 interacts with and regulates the phosphorylation level of OsMAPK6, which is known to regulate cell division and grain size in rice. Thus, our findings suggest OsRac1 modulates rice grain size and yield by influencing cell division. This study provides insights into the molecular mechanisms underlying the control of rice grain size and suggests that OsRac1 could serve as a potential target gene for breeding high-yield crops.

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Phenotypic plasticity of yield and related traits in rainfed durum wheat

The Journal of Agricultural Science ◽

10.1017/s0021859613000580 ◽

2013 ◽

Vol 152 (6) ◽

pp. 873-884 ◽

Cited By ~ 2

Author(s):

R. MOHAMMADI

Keyword(s):

Phenotypic Plasticity ◽

Durum Wheat ◽

Environmental Conditions ◽

Linear Models ◽

Agronomic Traits ◽

Grain Weight ◽

High Yield ◽

Yield Improvement ◽

Modern Cultivar ◽

Breeding Lines

SUMMARYRainfall and temperature are unpredictable in Mediterranean environments, which results in inconsistent environmental conditions for crop growth and a critical source of uncertainty for farmers and growers. The objectives of the present study were to: (i) quantify and compare the plasticity of durum breeding lines, a modern cultivar and landraces on the basis of yield and agronomic traits and (ii) study associations between plasticity of yield and plasticity of agronomic and phenological traits. Plasticity was quantified using linear models for 11 durum breeding lines, one modern cultivar and two landraces grown in 21 diversified environments. The results showed that the effects due to environment, genotype and genotype×environment (G×E) interaction were significant, which indicates the existence of differences among genotypes for plasticity. Yield ranged from 1939 to 2419 kg/ha across environments and the range of plasticity was 0·66–1·13. The breeding lines and the modern cultivar had higher grain yields compared with the landraces at the same level of plasticity. The landraces with below-average plasticity in yield were characterized as tall in stature and late in heading and maturity, whereas the breeding lines and modern cultivar with above-average plasticity in yield were early in heading and maturity, semi-dwarf and high-yielding, which indicates the success in breeding the materials for unpredictable environmental conditions. In conclusion, yield plasticity was associated with yield improvement and high yield plasticity tends to associate with earliness, shorter plants and low grain weight.

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