scholarly journals Identification of cold tolerance QTLs at the bud burst stage in 211 rice landraces by GWAS

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Caijing Li ◽  
Jindong Liu ◽  
Jianxin Bian ◽  
Tao Jin ◽  
Baoli Zou ◽  
...  
Keyword(s):  
Low Temperature ◽  
Cold Tolerance ◽  
Natural Population ◽  
Genetic Basis ◽  
Bud Burst ◽  
Rice Varieties ◽  
Rice Landraces ◽  
Population Structure Analysis ◽  
A Genome ◽  
First Time

Abstract Background Rice is a crop that is very sensitive to low temperature, and its morphological development and production are greatly affected by low temperature. Therefore, understanding the genetic basis of cold tolerance in rice is of great significance for mining favorable genes and cultivating excellent rice varieties. However, there have been limited studies focusing on cold tolerance at the bud burst stage; therefore, considerable attention should be given to the genetic basis of cold tolerance at this stage. Results In this study, a natural population consisting of 211 rice landraces collected from 15 provinces in China and other countries was used for the first time to evaluate cold tolerance at the bud burst stage. Population structure analysis showed that this population was divided into two groups and was rich in genetic diversity. Our evaluation results confirmed that japonica rice was more tolerant to cold at the bud burst stage than indica rice. A genome-wide association study (GWAS) was performed with the phenotypic data of 211 rice landraces and a 36,727 SNP dataset under a mixed linear model. Twelve QTLs (P < 0.0001) were identified for the seedling survival rate (SR) after treatment at 4 °C, in which there were five QTLs (qSR2–2, qSR3–1, qSR3–2, qSR3–3 and qSR9) that were colocalized with those from previous studies and seven QTLs (qSR2–1, qSR3–4, qSR3–5, qSR3–6, qSR3–7, qSR4 and qSR7) that were reported for the first time. Among these QTLs, qSR9, harboring the most significant SNP, explained the most phenotypic variation. Through bioinformatics analysis, five genes (LOC_Os09g12440, LOC_Os09g12470, LOC_Os09g12520, LOC_Os09g12580 and LOC_Os09g12720) were identified as candidates for qSR9. Conclusion This natural population consisting of 211 rice landraces combined with high-density SNPs will serve as a better choice for identifying rice QTLs/genes in the future, and the detected QTLs associated with cold tolerance at the bud burst stage in rice will be conducive to further mining favorable genes and breeding rice varieties under cold stress.

scholarly journals Genome-Wide Association Study (GWAS) For Cold Tolerance at The Bud Burst Stage in Rice Using SNP Markers

2021 ◽  
Author(s):  
Caijing Li ◽  
Jindong Liu ◽  
Jianxin Bian ◽  
Tao Jin ◽  
Baoli Zou ◽  
...  
Keyword(s):  
Low Temperature ◽  
Association Study ◽  
Cold Tolerance ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Bud Burst ◽  
Rice Varieties ◽  
Rice Landraces ◽  
Genome Wide

Abstract Background: Rice is a crop that is very sensitive to low temperature, and its morphological development and production are greatly affected by low temperature. Therefore, understanding the genetic basis of cold tolerance in rice is of great significance for mining favorable genes and cultivating excellent rice varieties. However, there were limited studies focusing on cold tolerance at the bud burst stage, therefore, considerable attention should be paid to the genetic basis of cold tolerance at the bud burst stage (CTBB).Results: In this study, a natural population consisting of 211 rice landraces collected from 15 provinces of China and other countries were firstly used to evaluate the cold tolerance at the bud burst stage. Population structure analysis showed that this population divided into three groups and was rich in genetic diversity. Our evaluation results confered that the japonica rice was more tolerance to cold at the bud burst stage than indica rice. Genome-wide association study (GWAS) were performed through the phenotypic data of 211 rice landraces and 36,727 SNPs dataset under a mixed linear model, and 12 QTLs (P < 0.0001) were identified according to the seedling survival rate (SSR) treated at 4 ℃, in which there are five QTLs (qSSR2-2, qSSR3-1, qSSR3-2, qSSR3-3 and qSSR9) which were co-located with previous studies, and seven QTLs (qSSR2-1, qSSR3-4, qSSR3-5, qSSR3-6, qSSR3-7, qSSR4 and qSSR7) which were reported for the first time. Among these QTLs, qSSR9, harboring the highest-peak SNP, explained biggest phenotypic variation. Through bioinformatics analysis, five genes (LOC_Os09g12440, LOC_Os09g12470, LOC_Os09g12520, LOC_Os09g12580 and LOC_Os09g12720) were nominated as candidates for qSSR9. Conclusion: This natural population consisting of 211 rice landraces with high density SNPs will serve as a better choice for identifying rice QTLs/genes in future, and the detected QTLs associated with cold tolerance in rice bud burst stage will be conducive to further mining favorable genes and breeding of rice varieties under cold stress.

Cold tolerance in rice varieties at different growth stages

2009 ◽  
Vol 60 (4) ◽  
pp. 328 ◽  
Author(s):  
C. Ye ◽  
S. Fukai ◽  
I. Godwin ◽  
R. Reinke ◽  
P. Snell ◽  
...  
Keyword(s):  
Low Temperature ◽  
Cold Tolerance ◽  
High Elevation ◽  
Temperature Tolerance ◽  
Seedling Stage ◽  
Growth Stages ◽  
Rice Varieties ◽  
Low Temperature Tolerance ◽  
Wide Range ◽  
Different Growth Stages

Low temperature is a common production constraint in rice cultivation in temperate zones and high-elevation environments, with the potential to affect growth and development from germination to grain filling. There is a wide range of genotype-based differences in cold tolerance among rice varieties, these differences often reflecting growth conditions in the place of origin, as well as breeding history. However, improving low temperature tolerance of varieties has been difficult, due to a lack of clarity of the genetic basis to low temperature tolerance for different growth stages of the rice plant. Seeds or plants of 17 rice varieties of different origins were exposed to low temperature during germination (15°C), seedling, booting, and flowering stages (18.5°C), to assess their cold tolerance at different growth stages. Low temperature at the germination stage reduced both the percentage and speed of germination. Varieties from China (B55, Banjiemang, and Lijianghegu) and Hungary (HSC55) were more tolerant of low temperature than other varieties. Most of the varieties showed moderate levels of low temperature tolerance during the seedling stage, the exceptions being some varieties from Australia (Pelde, YRL39, and YRM64) and Africa (WAB160 and WAB38), which were susceptible to low temperature at the seedling stage. Low temperature at booting and flowering stages reduced plant growth and caused a significant decline in spikelet fertility. Some varieties from China (B55, Bangjiemang, Lijiangheigu), Japan (Jyoudeki), the USA (M103, M104), and Australia (Quest) were tolerant or moderately tolerant, while the remaining varieties were susceptible or moderately susceptible to low temperature at booting and flowering stages. Three varieties from China (B55, Lijianghegu, Banjiemang) and one from Hungary (HSC55) showed consistent tolerance to low temperature at all growth stages. These varieties are potentially important gene donors for breeding and genetic studies. The cold tolerance of the 17 rice varieties assessed at different growth stages was correlated. Screening for cold tolerance during early growth stages can therefore potentially be an effective way for assessing cold tolerance in breeding programs.

scholarly journals Genome-Wide Association Studies of Leaf Angle in Maize

2021 ◽  
Author(s):  
Bo Peng ◽  
Xiaolei Zhao ◽  
Yi Wang ◽  
Chunhui Li ◽  
Yongxiang Li ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Phenotypic Variation ◽  
Genetic Basis ◽  
Genome Wide Association ◽  
Leaf Angle ◽  
Genome Wide Association Studies ◽  
Major Qtls ◽  
Genome Wide ◽  
Population Structure Analysis ◽  
A Genome

Abstract Compact plant-type with small leaf angle has increased canopy light interception, which is conducive to the photosynthesis of the population and higher population yield at high density planting in maize. In this study, a panel of 285 diverse maize inbred lines genotyped with 56,000 SNPs was used to investigate the genetic basis of leaf angle across three consecutive years using a genome-wide association study (GWAS). The leaf angle showed broad phenotypic variation and high heritability across different years. Population structure analysis subdivided the panel into four subgroups that correspond to the four major empirical germplasm origins in China, i.e., Tangsipingtou, Reid, Lancaster and P. When tested with the optimal GWAS model, we found that the Q+K model was the best in reducing false positive. In total, 96 SNPs accounting for 5.54%-10.44% of phenotypic variation were significantly (P<0.0001) associated with leaf angle across three years. According to the linkage disequilibrium decay distance, 96 SNPs were binned in 43 QTLs for leaf angle. Seven major QTLs with R2>8% stably detected in at least two years and BLUP values were clustered in four genomic regions (bins 2.01, 2.07, 5.06, and 10.04). Seven important candidate genes, Zm00001d001961, Zm00001d006348, Zm00001d006463, Zm00001d017618, Zm00001d024919, Zm00001d025018, and Zm00001d025033 were predicted for the seven stable major QTLs, respectively. The markers identified in this study can be used for molecular breeding for leaf angle, and the candidate genes would contribute to further understanding of the genetic basis of leaf angle.

scholarly journals Identification of candidate genes for gelatinization temperature, gel consistency and pericarp color by GWAS in rice based on SLAF-sequencing

2018 ◽  
Author(s):  
Xinghai Yang ◽  
Xiuzhong Xia ◽  
Yu Zeng ◽  
Baoxuan Nong ◽  
Zongqiong Zhang ◽  
...  
Keyword(s):  
Population Structure ◽  
Phenotypic Variation ◽  
Genetic Basis ◽  
Chromosome 3 ◽  
Chromosome 6 ◽  
Gelatinization Temperature ◽  
Rice Landraces ◽  
Population Structure Analysis ◽  
Pericarp Color ◽  
Gel Consistency

AbstractRice is an important cereal in the world, uncovering the genetic basis of agronomic traits in rice landraces genes associated with agronomically important traits is indispensable for both understanding the genetic basis of phenotypic variation and efficient crop improvement. Gelatinization temperature, gel consistency and pericarp color are important indices of rice cooking and eating quality evaluation and potential nutritional importance, which attract wide attentions in the application of genetic and breeding. To dissect the genetic basis of gelatinization temperature (GT), gel consistency (GC) and pericarp color (PC), a total of 419 rice landraces core germplasm collections consisting of 330 indica lines, 78 japonica lines and 11 uncertain varieties were grown, collected, then GT, GC, PC were measured for two years, and sequenced using Specific Locus Amplified Fragment Sequencing (SLAF) technology. In this study, 261,385,070 clean reads and 56,768 polymorphic SLAF tags were obtained, which a total of 211,818 single nucleotide polymorphisms (SNPs) were discovered. With 208,993 SNPs meeting the criterion of minor allele frequency (MAF) > 0.05 and integrity> 0.5, the phylogenetic tree and population structure analysis were performed for all 419 rice landraces, and the whole panel mainly separated into six subpopulations based on population structure analysis. Genome-wide association study (GWAS) was carried out for the whole panel, indica subpanel and japonica subpanel with subset SNPs respectively. One quantitative trait locus (QTL) on chromosome 6 for GT was detected in the whole panel and indica subpanel, and one QTL associated with GC was located on chromosome 6 in the whole panel and indica subpanel. For the PC trait, 8 QTLs were detected in the whole panel on chromosome 1, 3, 4, 7, 8, 10 and 11, and 7 QTLs in the indica subpanel on chromosome 3, 4, 7, 8, 10 and 11. The loci on chromosome 3, 8, 10 and 11 have not been identified previously, and they may be the candidate genes of pericarp color. For the three traits, no QTL was detected in japonica subpanel probably because of the polymorphism repartition between the subpanel, or small population size of japonica subpanel. This paper provides new gene resources and insights into the molecular mechanisms of important agricultural trait of rice phenotypic variation and genetic improvement of rice quality variety breeding.

scholarly journals Genet assignment and population structure analysis in a clonal forest-floor herb, Cardamine leucantha, using RAD-seq

AoB Plants ◽  
2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Michiaki Tsujimoto ◽  
Kiwako S Araki ◽  
Mie N Honjo ◽  
Masaki Yasugi ◽  
Atsushi J Nagano ◽  
...  
Keyword(s):  
Natural Population ◽  
Draft Genome ◽  
Clonal Plant ◽  
Genetic Distances ◽  
Plant Populations ◽  
Population Structure Analysis ◽  
Dna Microsatellite ◽  
First Time ◽  
Simple Sequence

Abstract To study the genetic structure of clonal plant populations, genotyping and genet detection using genetic markers are necessary to assign ramets to corresponding genets. Assignment is difficult as it involves setting a robust threshold of genetic distance for genet distinction as neighbouring genets in a plant population are often genetically related. Here, we used restriction site-associated DNA sequencing (RAD-seq) for a rhizomatous clonal herb, Cardamine leucantha [Brassicaceae] to accurately determine genet structure in a natural population. We determined a draft genome sequence of this species for the first time, which resulted in 66 617 scaffolds with N50 = 6086 bp and an estimated genome size of approximately 253 Mbp. Using genetic distances based on the RAD-seq analysis, we successfully distinguished ramets that belonged to distinct genets even from a half-sib family. We applied these methods to 372 samples of C. leucantha collected at 1-m interval grids within a 20 × 20 m plot in a natural population in Hokkaido, Japan. From these samples, we identified 61 genets with high inequality in terms of genet size and patchy distribution. Spatial autocorrelation analyses indicated significant aggregation within 7 and 4 m at ramet and genet levels, respectively. An analysis of parallel DNA microsatellite loci (simple sequence repeats) suggested that RAD-seq can provide data that allows robust genet assignment. It remains unclear whether the large genets identified here became dominant stochastically or deterministically. Precise identification of genets will assist further study and characterization of dominant genets.

scholarly journals Natural population re-sequencing detects the genetic basis of local adaptation to low temperature in a woody plant

2020 ◽  
Author(s):  
Yanmin Hu ◽  
Xianjun Peng ◽  
Fenfen Wang ◽  
Peilin Chen ◽  
Meiling Zhao ◽  
...  
Keyword(s):  
Low Temperature ◽  
Local Adaptation ◽  
Natural Population ◽  
Genetic Basis ◽  
Woody Plant

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.

scholarly journals Genome-wide association study of cold tolerance of Chinese indica rice varieties at the bud burst stage

2018 ◽  
Vol 37 (3) ◽  
pp. 529-539 ◽  
Author(s):  
Mengchen Zhang ◽  
Jing Ye ◽  
Qun Xu ◽  
Yue Feng ◽  
Xiaoping Yuan ◽  
...  
Keyword(s):  
Association Study ◽  
Cold Tolerance ◽  
Genome Wide Association Study ◽  
Indica Rice ◽  
Genome Wide Association ◽  
Bud Burst ◽  
Rice Varieties ◽  
Genome Wide

scholarly journals Genetic basis analysis for indica germinability under low temperature using a new RILs population genotyping by whole-genome resequencing

2020 ◽  
Author(s):  
Peng Wang ◽  
Guangliang Wu ◽  
Xin Luo ◽  
Ruiqi Liu ◽  
Andong Zhou ◽  
...  
Keyword(s):  
Cold Stress ◽  
Cold Tolerance ◽  
Genetic Map ◽  
Marker Assisted Selection ◽  
Genetic Basis ◽  
High Density ◽  
Genome Resequencing ◽  
Rice Varieties ◽  
Whole Genome Resequencing ◽  
Germination Stage

Abstract Background : Improving the cold tolerance of rice at germination stage is an important objective to maintain rice yields. However, less analyses were carried out to detect the quantitative trait loci (QTLs) associated with cold tolerance using indica/indica population. Therefore, the genetic basis of cold tolerance of the indica varieties should be provided considerable attentionResults: In this study, a recombinant inbred lines (RILs) population comprising 126 lines derived from two widely used double-cropped indica rice varieties Wufeng B (WFB) and Changhui T025 (CHT025) was used to construct a high-density linkage map based on whole-genome resequencing. The high-density genetic map included 2,578 bins on 12 linkage groups and was 1762.80 cM in length, with an average interlocus distance of 0.68 cM. On the basis of newly constructed high-density genetic map, a total of 18 additive QTLs ranging from 34.55 to 315.21 kb on Nipponbare genome and two pairs of epistatic QTLs associated with cold stress at germination stage were detected, which indicated that the genetic basis of cold tolerance of WFB and CHT025 at germination stage is manly due to additive effects of several QTLs. Otherwise, the phylogenetic analysis showed that WFB is a typical indica variety while CHT025 is an interphyletic rice variety. Most of the favorable QTLs harbouring in indica WFB showed different chromosomal region from the QTLs associating with cold stress from japonica rice in previous studies, which indicated that indica might have different cold stress genetic mechanism comparing to japonica subspecies. Furthermore, we can incorporate these favorable QTLs existing in WFB into rice varieties to breed new cold tolerance indica male sterile maintenance line via marker-assisted selection; CHT025 is a better source of these cold tolerance favorable QTLs only only for the improvement of indcia but also for japonica restorer line germinability under low temperature via marker-assisted selection.Conclusion : This population with high density genetic map will serve as better choice for identifying important quantitative traits of these two good indica germplasms, and these favorable QTLs exist in WFB and CHT025 can be used to breed new cold tolerance indica varieties via marker-assisted selection. These authors have contributed equally to this work

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