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

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.

Defining a holoprosencephaly locus on human chromosome 14q13 and characterization of potential candidate genes

Genomics ◽  
2005 ◽  
Vol 85 (5) ◽  
pp. 608-621 ◽  
Author(s):  
Deepak Kamnasaran ◽  
Chih-Ping Chen ◽  
Koenraad Devriendt ◽  
Lakshmi Mehta ◽  
Diane W. Cox
Keyword(s):  
Human Chromosome ◽  
Candidate Genes ◽  
Potential Candidate

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.

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

2006 ◽  
Vol 57 (7) ◽  
pp. 771 ◽  
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.

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 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.

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