scholarly journals Identification and Validation of a QTL for Bacterial Leaf Streak Resistance in Rice (Oryza sativa L.) against Thai Xoc Strains

Genes ◽  
2021 ◽  
Vol 12 (10) ◽  
pp. 1587
Author(s):  
Tripop Thianthavon ◽  
Wanchana Aesomnuk ◽  
Mutiara K. Pitaloka ◽  
Wannapa Sattayachiti ◽  
Yupin Sonsom ◽  
...  
Keyword(s):  
Candidate Gene ◽  
Oryza Sativa L ◽  
Genomic Region ◽  
Phenotypic Variance ◽  
Potential Candidate ◽  
Nucleotide Polymorphisms ◽  
Bacterial Leaf Streak ◽  
Rice Varieties ◽  
F2 Population ◽  
Specific Pcr

Rice is one of the most important food crops in the world and is of vital importance to many countries. Various diseases caused by fungi, bacteria and viruses constantly threaten rice plants and cause yield losses. Bacterial leaf streak disease (BLS) caused by Xanthomonas oryzae pv. oryzicola (Xoc) is one of the most devastating rice diseases. However, most modern rice varieties are susceptible to BLS. In this study, we applied the QTL-seq approach using an F2 population derived from the cross between IR62266 and Homcholasit (HSC) to rapidly identify the quantitative trait loci (QTL) that confers resistance to BLS caused by a Thai Xoc isolate, SP7-5. The results showed that a single genomic region at the beginning of chromosome 5 was highly associated with resistance to BLS. The gene xa5 was considered a potential candidate gene in this region since most associated single nucleotide polymorphisms (SNPs) were within this gene. A Kompetitive Allele-Specific PCR (KASP) marker was developed based on two consecutive functional SNPs in xa5 and validated in six F2 populations inoculated with another Thai Xoc isolate, 2NY2-2. The phenotypic variance explained by this marker (PVE) ranged from 59.04% to 70.84% in the six populations. These findings indicate that xa5 is a viable candidate gene for BLS resistance and may help in breeding programs for BLS resistance.

scholarly journals Identification of candidate genes controlling chilling tolerance of rice in the cold region at the booting stage by BSA-Seq and RNA-Seq

2020 ◽  
Vol 7 (11) ◽  
pp. 201081
Author(s):  
Zhenhua Guo ◽  
Lijun Cai ◽  
Zhiqiang Chen ◽  
Ruiying Wang ◽  
Lanming Zhang ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Bulked Segregant Analysis ◽  
Expression Patterns ◽  
Enrichment Analysis ◽  
Chilling Tolerance ◽  
Pathway Enrichment Analysis ◽  
Potential Candidate ◽  
Rice Varieties ◽  
Booting Stage ◽  
F2 Population

Rice is sensitive to low temperatures, specifically at the booting stage. Chilling tolerance of rice is a quantitative trait loci that is governed by multiple genes, and thus, its precise identification through the conventional methods is an arduous task. In this study, we investigated the candidate genes related to chilling tolerance at the booting stage of rice. The F2 population was derived from Longjing25 (chilling-tolerant) and Longjing11 (chilling-sensitive) cross. Two bulked segregant analysis pools were constructed. A 0.82 Mb region containing 98 annotated genes on chromosomes 6 and 9 was recognized as the candidate region associated with chilling tolerance of rice at the booting stage. Transcriptomic analysis of Longjing25 and Longjing11 revealed 50 differentially expressed genes (DEGs) on the candidate intervals. KEGG pathway enrichment analysis of DEGs was performed. Nine pathways were found to be enriched, which contained 10 DEGs. A total of four genes had different expression patterns or levels between Longjing25 and Longjing11. Four out of the 10 DEGs were considered as potential candidate genes for chilling tolerance. This study will assist in the cloning of the candidate genes responsible for chilling tolerance and molecular breeding of rice for the development of chilling-tolerant rice varieties.

scholarly journals In silico analysis of the fragrance gene (badh2) in Asian rice (Oryza sativa L.) germplasm and validation of allele specific markers

2020 ◽  
Vol 18 (2) ◽  
pp. 71-80
Author(s):  
Withanage Vidyani Erandika Withana ◽  
Rathanyaka Maudiyanselage Ramesha Eshani Kularathna ◽  
Nisha Sualri Kottearachchi ◽  
Deepthika S. Kekulandara ◽  
Jagath Weerasena ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
In Silico ◽  
Oryza Sativa L ◽  
Major Gene ◽  
In Silico Analysis ◽  
Betaine Aldehyde Dehydrogenase ◽  
Nucleotide Polymorphisms ◽  
Rice Varieties ◽  
Asian Rice ◽  
Allele Specific

AbstractBadh2 of rice is considered to be the major gene responsible for the fragrance in rice. The wild type badh2 allele encodes betaine aldehyde dehydrogenase 2 (BADH2) enzyme while the mutated version of badh2 gene encodes non-functional BADH2 enzyme that leads to the accumulation of 2-acetyl-1-pyrroline (2AP), the principal fragrant compound in rice. There are many mutated recessive alleles causing fragrance in global rice germplasm, although the badh2.1 allele present in Basmati type rice is the most well-known among breeders. In this study, we attempted to reveal potential fragrance causing mutations, and the respective varieties carrying them, through in silico analysis based on the sequences available in the Rice SNP-Seek-Database of International Rice Research Institute. The sequences of 1878 rice accessions from 22 countries were analysed to identify mutations in each exon of badh2 comparatively with the non-fragrant ‘wildtype’ GenBank sequence in Nanjing11, Oryza sativa indica (EU770319.1). Results revealed that 63 varieties from 12 countries possessed the most prevalent allele, badh2.1 having an 8 bp deletion and three single nucleotide polymorphisms in the 7th exon. The second most prevalent allele in genotypes from Asia was badh2.7 having a ‘G’ insertion in the 14th exon. A novel allele with a T deletion in 9th exon was detected in a Thai rice accession. Rice varieties containing either badh2.1 or badh2.7 alleles could be identified with DNA markers for badh2.1 (frg) and badh2.7 (Bad2.7CAPS). The marker, Bad2.7CAPS, co-segregated with the fragrance phenotype in two crosses, confirming the possibility of employing it in marker assisted breeding.

scholarly journals Genetic Dissection of Seed Storability and Validation of Candidate Gene Associated with Antioxidant Capability in Rice (Oryza sativa L.)

2019 ◽  
Vol 20 (18) ◽  
pp. 4442 ◽  
Author(s):  
Yuan ◽  
Fan ◽  
Xia ◽  
Ding ◽  
Tian ◽  
...  
Keyword(s):  
Candidate Gene ◽  
Oryza Sativa L ◽  
Recombinant Inbred Lines ◽  
Physiological Characteristic ◽  
Genetic Dissection ◽  
Isogenic Line ◽  
Single Nucleotide ◽  
F2 Population ◽  
Germination Ability ◽  
Seed Storability

Seed storability, defined as the ability to remain alive during storage, is an important agronomic and physiological characteristic, but the underlying genetic mechanism remains largely unclear. Here, we report quantitative trait loci (QTLs) analyses for seed storability using a high-density single nucleotide polymorphism linkage map in the backcross recombinant inbred lines that was derived from a cross of a japonica cultivar, Nipponbare, and an indica cultivar, 9311. Seven putative QTLs were identified for seed storability under natural storage, each explaining 3.6–9.0% of the phenotypic variation in this population. Among these QTLs, qSS1 with the 9311 alleles promoting seed storability was further validated in near-isogenic line and its derived-F2 population. The other locus (qSS3.1) for seed storability colocalized with a locus for germination ability under hydrogen peroxide, which is recognized as an oxidant molecule that causes lipid damage. Transgenic experiments validated that a candidate gene (OsFAH2) resides the qSS3.1 region controlling seed storability and antioxidant capability. Overexpression of OsFAH2 that encodes a fatty acid hydroxylase reduced lipid preoxidation and increased seed storability. These findings provide new insights into the genetic and physiological bases of seed storability and will be useful for the improvement of seed storability in rice.

scholarly journals QTL mapping and genome-wide prediction of heat tolerance in multiple connected populations of temperate maize

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Delphine Van Inghelandt ◽  
Felix P. Frey ◽  
David Ries ◽  
Benjamin Stich
Keyword(s):  
Qtl Mapping ◽  
Heat Tolerance ◽  
Prediction Models ◽  
Genotypic Diversity ◽  
Phenotypic Variance ◽  
Nucleotide Polymorphisms ◽  
Prediction Ability ◽  
Specific Pcr ◽  
Genome Wide ◽  
Trait Locus

Abstract Climate change will lead to increasing heat stress in the temperate regions of the world. The objectives of this study were the following: (I) to assess the phenotypic and genotypic diversity of traits related to heat tolerance of maize seedlings and dissect their genetic architecture by quantitative trait locus (QTL) mapping, (II) to compare the prediction ability of genome-wide prediction models using various numbers of KASP (Kompetitive Allele Specific PCR genotyping) single nucleotide polymorphisms (SNPs) and RAD (restriction site-associated DNA sequencing) SNPs, and (III) to examine the prediction ability of intra-, inter-, and mixed-pool calibrations. For the heat susceptibility index of five of the nine studied traits, we identified a total of six QTL, each explaining individually between 7 and 9% of the phenotypic variance. The prediction abilities observed for the genome-wide prediction models were high, especially for the within-population calibrations, and thus, the use of such approaches to select for heat tolerance at seedling stage is recommended. Furthermore, we have shown that for the traits examined in our study, populations created from inter-pool crosses are suitable training sets to predict populations derived from intra-pool crosses.

scholarly journals Mapping of Qtl for Anaerobic Germination Using the Donor Ac39416a in the Genetic Background of Swarna Sub-1 (Oryza Sativa L.)

2021 ◽  
Author(s):  
BOLLINENI SAIMOHAN ◽  
N. Chamundeswari ◽  
T. Haritha ◽  
N. Veronica
Keyword(s):  
Ssr Markers ◽  
Oryza Sativa L ◽  
Phenotypic Variance ◽  
Rice Varieties ◽  
Seeding Method ◽  
Anaerobic Germination ◽  
Individual Contributions ◽  
Important Trait ◽  
The Mean ◽  
Integrated Software

Abstract Background: Anaerobic germination is an important trait in particular for cultivation under direct seeding method in kharif season, as well as during nursery rising for transplant rice, as sometimes unexpected rains immediately after sowing will drastically reduce the plant population.Methods and Results: In the present investigation phenotypic screening for Anaerobic germination (AG) was carried out using 188 F2:3 population of Swarna Sub1/AC39416A at RARS (APRRI), Maruteru. The mean anaerobic germination per cent recorded after the two weeks of submergence ranged from 0% to 95% with overall mean of 47.51% whereas, for three weeks of submergence, the mean anaerobic germination per cent recorded between 0 and 95%, with overall mean of 37.66%. 134 (19.42%) out of 687 Simple Sequence Repeats (SSR) markers surveyed were polymorphic between the parents. Linkage analysis was done with 83 SSR markers showing polymorphism clearly using the integrated software called QTL IciMapping software version 4.1.0. The length of linkage map constructed across whole genome was 3600.8 cM and identified seven QTLs viz., qAG2, qAG3, qAG7-1, qAG7-2, qAG9, qAG10 and qAG12. All these seven QTLs explained phenotypic variance of about 37.47% collectively for AG trait, with their individual contributions ranging from 3.5% to 8.67% of phenotypic variation and LOD scores of 2.6 to 5.86. The LOD score and phenotypic variance is 5.86 and 8.67% respectively for qAG10 a novel QTL identified in the present study using ICIM method. Conclusion: QTL “qAG12-1” identified in this study may be considered for introgression into popular elite rice varieties otherwise susceptible for anaerobic germination after fine mapping studies.

Using the RTM-GWAS procedure to detect the drought tolerance QTL-allele system at the seedling stage under sand culture in a half-sib population of soybean [Glycine max(L.) Merr.]

2019 ◽  
Vol 99 (6) ◽  
pp. 801-814 ◽  
Author(s):  
Mueen Alam Khan ◽  
Fei Tong ◽  
Wubin Wang ◽  
Jianbo He ◽  
Tuanjie Zhao ◽  
...  
Keyword(s):  
Drought Tolerance ◽  
Genetic Architecture ◽  
Genome Wide Association Study ◽  
Weighted Average ◽  
Dry Weight ◽  
Sand Culture ◽  
Phenotypic Variance ◽  
Potential Candidate ◽  
Nucleotide Polymorphisms ◽  
Average Value

Soybean crops face drought as one of their major yield barriers. Dissecting the complete genetic architecture of drought tolerance (DT) is an ongoing challenge for soybean breeders. A half-sib population with 404 lines consisting of two recombinant inbred line (RIL) populations with M8206 as the joint parent (M8206 × TongShan and ZhengYang × M8206) was established and tested for their DT under sand culture. The population was sequenced using RAD-seq (restriction-site-associated DNA sequencing) filtered with minor allele frequency (MAF) ≥ 0.01, and 55 936 single nucleotide polymorphisms (SNPs) were obtained and organized into 6137 SNPLDBs (SNP linkage disequilibrium blocks). The innovative RTM-GWAS (restricted two stage multi-locus genome-wide association study) identified 46 novel QTLs with 107 alleles on an average of 38.67% of the phenotypic variance (PV) collectively for relative plant length (RPL) and relative plant dry weight (RPDW). The identified quantitative trait loci (QTLs) with their corresponding alleles for RPL and RPDW were structured into QTL-allele matrices, showing the DT genetic architecture of the three parents and half-sib population. From the matrices, the possible best genotype was predicted to have their weighted average value (WAV) over two indicators 1.663, while the top 10 optimal crosses among RILs with 95thpercentile WAV was 0.872–0.960, transgressive over the parents (0.469–0.675) but much less than 1.663, depicting further pyramiding potential. From the detected QTL-allele system, 63 potential candidate genes collectively for both RPL and RPDW indicators explaining on average of 26.94% PV were annotated and χ2-tested as a DT potential candidate gene system involving nine biological processes, endorsing the genetic complexity of DT.

scholarly journals Developing KASP Markers for Identification of Basmati Rice Varieties

2020 ◽  
Author(s):  
Katherine Steele ◽  
Mark Quinton Tulloch ◽  
Malcolm Burns ◽  
Werner Nader
Keyword(s):  
Microsatellite Markers ◽  
Rice Genome ◽  
Basmati Rice ◽  
Nucleotide Polymorphisms ◽  
Rice Varieties ◽  
Specific Pcr ◽  
Wide Range ◽  
Allele Specific ◽  
Allele Specific Pcr ◽  
Kasp Markers

Abstract Authentication of Basmati rice has relied on microsatellite markers since 2004, but microsatellites cannot distinguish between all of the forty-one Basmati varieties approved in 2017. This study investigated whether single nucleotide polymorphisms (SNP) and insertion/deletion (InDel) variations developed into KASP™ (Kompetitive Allele Specific PCR; LGC Biosearch Technologies) could be used to distinguish between commercial Basmati varieties. Suitable loci were identified by comparing whole genome sequences of 120 diverse rice accessions. Sequences flanking these loci were standardized across a wide range of rice genomes to produce optimal KASP designs. We selected 364 KASP designs to use for genotyping; they were either near to informative microsatellite markers, within the Badh2 and Waxy genes, or distributed throughout the rice genome. Genotypes for 327 KASP were obtained with 255 loci revealing polymorphism in up to 41 samples of approved Basmati varieties and 20 non-Basmati varieties. The varieties genotyped had not been used in the KASP design process. KASP were able to distinguish between commercial Basmati varieties that could not be distinguished with currently available microsatellites. Thirty-seven Basmati varieties could be distinguished from all others with between 3 and 8 KASP markers out of a pool of 98 informative markers. A reduced set of 24 KASP markers could determine whether a sample belongs to one of eight family groups. All of the KASP markers used in this study can be purchased from LGC Biosearch Technologies. These markers have potential to be used by industry for routine testing and regulation.

scholarly journals An SNP-Based Genetic Map and QTL Mapping for Growth Traits in the Red-Spotted Grouper (Epinephelus akaara)

Genes ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 793 ◽  
Author(s):  
Wang ◽  
Jiang ◽  
Zheng ◽  
Xiao ◽  
Zhang ◽  
...  
Keyword(s):  
Genetic Map ◽  
First Generation ◽  
Growth Traits ◽  
Survival Rates ◽  
Larval Survival ◽  
Phenotypic Variance ◽  
Potential Candidate ◽  
Nucleotide Polymorphisms ◽  
Epinephelus Akaara ◽  
Genetic Length

The red-spotted grouper (Epinephelus akaara) is one of the most commercially important aquatic species in China. However, its seedstock has low larval survival rates, and its stability is confronted with the danger of overexploitation. In this study, a high-density genetic map was constructed using 3435 single nucleotide polymorphisms (SNPs) from 142 first generation (F1) full-sib offspring and two parents of a red-spotted grouper population. The total genetic length of the map was 2300.12 cM with an average intermarker distance of 0.67 cM. Seventeen genome-wide significant quantitative trait loci (QTLs) for growth-related traits were detected on 24 linkage groups, including 5 QTLs for full length, 7 QTLs for body length, and 5 QTLs for body weight. The contribution values of explained phenotypic variance ranged from 10.7% to 12.9%. Moreover, 13 potential candidate genes for growth-related traits were identified. Collectively, these findings will be useful for conducting marker-assisted selection of the red-spotted grouper in future studies.

scholarly journals Identification of Candidate Genes Conferring Cold Tolerance to Rice (Oryza sativa L.) at the Bud-Bursting Stage Using Bulk Segregant Analysis Sequencing and Linkage Mapping

2021 ◽  
Vol 12 ◽  
Author(s):  
Luomiao Yang ◽  
Lei Lei ◽  
Peng Li ◽  
Jingguo Wang ◽  
Chao Wang ◽  
...  
Keyword(s):  
Low Temperature ◽  
Cold Tolerance ◽  
Oryza Sativa L ◽  
Chromosome 9 ◽  
Pcr Analysis ◽  
Potential Candidate ◽  
Sequencing Data ◽  
Coding Region ◽  
Rice Varieties ◽  
Major Qtl

Low-temperature tolerance during the bud-bursting stage is an important characteristic of direct-seeded rice. The identification of cold-tolerance quantitative trait loci (QTL) in species that can stably tolerate cold environments is crucial for the molecular breeding of rice with such traits. In our study, high-throughput QTL-sequencing analyses were performed in a 460-individual F2:3 mapping population to identify the major QTL genomic regions governing cold tolerance at the bud-bursting (CTBB) stage in rice. A novel major QTL, qCTBB9, which controls seed survival rate (SR) under low-temperature conditions of 5°C/9 days, was mapped on the 5.40-Mb interval on chromosome 9. Twenty-six non-synonymous single-nucleotide polymorphism (nSNP) markers were designed for the qCTBB9 region based on re-sequencing data and local QTL mapping conducted using traditional linkage analysis. We mapped qCTBB9 to a 483.87-kb region containing 58 annotated genes, among which six predicted genes contained nine nSNP loci. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) analysis revealed that only Os09g0444200 was strongly induced by cold stress. Haplotype analysis further confirmed that the SNP 1,654,225 bp in the Os09g0444200 coding region plays a key role in regulating the cold tolerance of rice. These results suggest that Os09g0444200 is a potential candidate for qCTBB9. Our results are of great significance to explore the genetic mechanism of rice CTBB and to improve the cold tolerance of rice varieties by marker-assisted selection.

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