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

Rice ◽  
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.

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

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.

scholarly journals Validation of a QTL for Grain Size and Weight Using an Introgression Line from a Cross Between Oryza Sativa and Oryza Minuta

2020 ◽  
Author(s):  
Yue Feng ◽  
Xiaoping Yuan ◽  
Yiping Wang ◽  
Yaolong Yang ◽  
Mengchen Zhang ◽  
...  
Keyword(s):  
Grain Size ◽  
Oryza Sativa ◽  
Introgression Line ◽  
Chromosome 7 ◽  
Rice Grain ◽  
Phenotypic Variance ◽  
Oryza Minuta ◽  
Wild Rice Species ◽  
Electron Microscopy Analysis ◽  
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. A total of 12 QTLs for the five grain traits were identified on chromosomes 1, 2, 3, 6, 7, and 8. The QTL qGL7 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. 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. 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.

Dissection of Closely Linked QTLs Controlling Grain Size in Rice

2021 ◽  
Author(s):  
Pao Xue ◽  
Yu-yu Chen ◽  
Xiao-xia Wen ◽  
Bei-fang Wang ◽  
Qin-qin Yang ◽  
...  
Keyword(s):  
Grain Size ◽  
Genetic Resources ◽  
Candidate Genes ◽  
Cell Expansion ◽  
Grain Weight ◽  
Cytological Observation ◽  
Yield Improvement ◽  
Transcript Levels ◽  
Grain Width ◽  
Successive Generations

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.

scholarly journals Correction to: Validation of a QTL for Grain Size and Weight Using an Introgression Line from a Cross between Oryza sativa and Oryza minuta

Rice ◽  
2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Yue Feng ◽  
Xiaoping Yuan ◽  
Yiping Wang ◽  
Yaolong Yang ◽  
Mengchen Zhang ◽  
...  
Keyword(s):  
Grain Size ◽  
Oryza Sativa ◽  
Introgression Line ◽  
Oryza Minuta

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

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.

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

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.

scholarly journals Utilization of a Wheat50K SNP Microarray-Derived High-Density Genetic Map for QTL Mapping of Plant Height and Grain Traits in Wheat

Plants ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 1167
Author(s):  
Dongyun Lv ◽  
Chuanliang Zhang ◽  
Rui Yv ◽  
Jianxin Yao ◽  
Jianhui Wu ◽  
...  
Keyword(s):  
Plant Height ◽  
Genetic Map ◽  
Phenotypic Variation ◽  
Control Plant ◽  
Snp Array ◽  
High Density ◽  
Grain Weight ◽  
Thousand Grain Weight ◽  
Grain Length ◽  
Grain Width

Plant height is significantly correlated with grain traits, which is a component of wheat yield. The purpose of this study is to investigate the main quantitative trait loci (QTLs) that control plant height and grain-related traits in multiple environments. In this study, we constructed a high-density genetic linkage map using the Wheat50K SNP Array to map QTLs for these traits in 198 recombinant inbred lines (RILs). The two ends of the chromosome were identified as recombination-rich areas in all chromosomes except chromosome 1B. Both the genetic map and the physical map showed a significant correlation, with a correlation coefficient between 0.63 and 0.99. However, there was almost no recombination between 1RS and 1BS. In terms of plant height, 1RS contributed to the reduction of plant height by 3.43 cm. In terms of grain length, 1RS contributed to the elongation of grain by 0.11 mm. A total of 43 QTLs were identified, including eight QTLs for plant height (PH), 11 QTLs for thousand grain weight (TGW), 15 QTLs for grain length (GL), and nine QTLs for grain width (GW), which explained 1.36–33.08% of the phenotypic variation. Seven were environment-stable QTLs, including two loci (Qph.nwafu-4B and Qph.nwafu-4D) that determined plant height. The explanation rates of phenotypic variation were 7.39–12.26% and 20.11–27.08%, respectively. One QTL, Qtgw.nwafu-4B, which influenced TGW, showed an explanation rate of 3.43–6.85% for phenotypic variation. Two co-segregating KASP markers were developed, and the physical locations corresponding to KASP_AX-109316968 and KASP_AX-109519968 were 25.888344 MB and 25.847691 MB, respectively. Qph.nwafu-4B, controlling plant height, and Qtgw.nwafu-4B, controlling TGW, had an obvious linkage relationship, with a distance of 7–8 cM. Breeding is based on molecular markers that control plant height and thousand-grain weight by selecting strains with low plant height and large grain weight. Another QTL, Qgw.nwafu-4D, which determined grain width, had an explanation rate of 3.43–6.85%. Three loci that affected grain length were Qgl.nwafu-5A, Qgl.nwafu-5D.2, and Qgl.nwafu-6B, illustrating the explanation rates of phenotypic variation as 6.72–9.59%, 5.62–7.75%, and 6.68–10.73%, respectively. Two QTL clusters were identified on chromosomes 4B and 4D.

scholarly journals Identification of a novel QTL and candidate gene associated with grain size using chromosome segment substitution lines in rice

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Dianwen Wang ◽  
Wenqiang Sun ◽  
Zhiyang Yuan ◽  
Qiang Sun ◽  
Kai Fan ◽  
...  
Keyword(s):  
Grain Size ◽  
Grain Yield ◽  
Genetic Basis ◽  
Grain Weight ◽  
Chromosome Segment ◽  
Thousand Grain Weight ◽  
Substitution Lines ◽  
Grain Length ◽  
Chromosome Segment Substitution Lines ◽  
Segment Substitution

AbstractRice is one of the staple crops in the world. Grain size is an important determinant of rice grain yield, but the genetic basis of the grain size remains unclear. Here, we report a set of chromosome segment substitution lines (CSSL) developed in the genetic background of the genome-sequenced indica cultivar Zhenshan 97. Genotyping of the CSSLs by single nucleotide polymorphism array shows that most carry only one or two segments introduced from the genome-sequenced japonica cultivar Nipponbare. Using this population and the high-density markers, a total of 43 quantitative trait loci were identified for seven panicle- and grain-related traits. Among these loci, the novel locus qGL11 for grain length and thousand-grain weight was validated in a CSSL-derived segregating population and finely mapped to a 25-kb region that contains an IAA-amido synthetase gene OsGH3.13, This gene exhibited a significant expression difference in the young panicle between the near-isogenic lines that carry the contrasting Zhenshan 97 and Nipponbare alleles at qGL11. Expression and sequence analyses suggest that this gene is the most likely candidate for qGL11. Furthermore, several OsGH3.13 mutants induced by a CRISPR/Cas9 approach in either japonica or indica exhibit an increased grain length and thousand-grain weight, thus enhancing the final grain yield per plant. These findings provide insights into the genetic basis of grain size for the improvement of yield potential in rice breeding programs.

scholarly journals A High-Density Genetic Linkage Map of SLAFs and QTL Analysis of Grain Size and Weight in Barley (Hordeum vulgare L.)

2020 ◽  
Vol 11 ◽  
Author(s):  
Yunxia Fang ◽  
Xiaoqin Zhang ◽  
Xian Zhang ◽  
Tao Tong ◽  
Ziling Zhang ◽  
...  
Keyword(s):  
Grain Size ◽  
Genetic Map ◽  
Genetic Linkage Map ◽  
Recombinant Inbred Lines ◽  
High Density ◽  
Phenotypic Variance ◽  
Thousand Grain Weight ◽  
Hordeum Vulgare L ◽  
Specific Locus ◽  
Grain Width

Grain size is an important agronomic trait determines yield in barley, and a high-density genetic map is helpful to accurately detect quantitative trait loci (QTLs) related to grain traits. Using specific-locus amplified fragment sequencing (SLAF-seq) technology, a high-density genetic map was constructed with a population of 134 recombinant inbred lines (RILs) deriving from a cross between Golden Promise (GP) and H602, which contained 12,635 SLAFs with 26,693 SNPs, and spanned 896.74 cM with an average interval of 0.07 cM on seven chromosomes. Based on the map, a total of 16 QTLs for grain length (GL), grain width and thousand-grain weight were detected on 1H, 2H, 4H, 5H, and 6H. Among them, a major QTL locus qGL1, accounting for the max phenotypic variance of 16.7% was located on 1H, which is a new unreported QTL affecting GL. In addition, the other two QTLs, qGL5 and qTGW5, accounting for the max phenotypic variances of 20.7 and 21.1%, respectively, were identified in the same region, and sequencing results showed they are identical to HvDep1 gene. These results indicate that it is a feasible approach to construct a high-quality genetic map for QTL mapping by using SLAF markers, and the detected major QTLs qGL1, qGL5, and qTGW5 are useful for marker-assisted selection (MAS) of grain size in barley breeding.

scholarly journals GENETIC VARIABILITY FOR GRAIN QUALITY TRAITS IN AROMATIC RICE (Oryza sativa L)

2011 ◽  
Vol 24 (2) ◽  
pp. 19-24
Author(s):  
Kaniz Fatema ◽  
M. G. Rasul ◽  
M. A. K. Mian ◽  
M. M. Rahman
Keyword(s):  
Genetic Variability ◽  
Amylose Content ◽  
Oryza Sativa L ◽  
Grain Weight ◽  
Aromatic Rice ◽  
Thousand Grain Weight ◽  
Grain Length ◽  
Gel Consistency ◽  
Rice Genotypes ◽  
1000 Grain Weight

Forty five aromatic rice genotypes were evaluated to assess the genetic variability and diversity on the basis of nine characters. Significant variations were observed among the genotypes for all the characters (grain breadth (mm), grain length (mm), grain L/B ratio, gelatinization temperature (score), gel consistency (mm), amylose content (%), protein content (%), 1000 grain weight (g) and grain yield per plant (g)) studied. High GCV, PCV, heritability and GA as observed in amylose content, grain length average and L/B ratio suggested that these three characters could be transmitted to the progeny. Multivariate analysis revealed that 45 genotypes were grouped into six clusters. There were marked variations in intra-cluster distances, which ranged from 0.482 to 7.851. The highest intra cluster mean for five traits (amylose content, width average, L/B ratio, length average, 1000 grain weight) was obtained from cluster I constituted 10 genotypes. Thousand grain weight and amylose content have been found to contribute maximum towards genetic diversity in 45 genotypes of aromatic rice.DOI: http://dx.doi.org/10.3329/bjpbg.v24i2.17002

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