scholarly journals Molecular and Phenotypic Characterization for Cold Tolerance in Rice (Oryza sativa L.)

2020 ◽  
Vol 23 (2) ◽  
pp. 1-15
Author(s):  
PS Biswas ◽  
H Khatun ◽  
M Anisuzzaman
Keyword(s):  
Cold Stress ◽  
Cold Tolerance ◽  
Oryza Sativa L ◽  
Gene Diversity ◽  
Reproductive Stage ◽  
Seedling Stage ◽  
Phenotypic Characterization ◽  
Breeding Lines ◽  
Upgma Dendrogram ◽  
Ssr Loci

Cold stress affects growth and development of rice plants from germination to reproductive stages. Thirty breeding lines/varieties including tolerant and susceptible check varieties were evaluated for cold tolerance at seedling and reproductive stage using artificially induced low temperature situations to understand the genetic relationship among them and to identify promising donors for cold tolerance. Three breeding lines, BR8253-9-3-4-3, IR77497-31-2-3-1and IR2266-42-6-2 demonstrated higher cold tolerance for the seedling stage (LD score <3.0). Molecular analysis revealed 68% genetic similarity among the genotypes. On average 64% of the breeding lines shared common alleles at any given locus ranging from 27% (RM22870) to 97% (RM186). UPGMA dendrogram showed that majority of the breeding lines showing 4-5 degrees of LD were grouped together. Two breeding lines, BR8258-7-1-5-2B2 and BR8258-7-1-5-2B3 having 86% common alleles showed low leaf discoloration (LD: 4) at seedling stage coupled with relatively low reduction in spikelet fertility (45.8% and 48.1%) and grain yield (43.3% and 39.1%). The gene diversity and PIC value revealed that seven SSR loci (RM1282, RM600, RM5349, RM6972, RM5847, RM5911, and RM511) might be the best markers to differentiate between tolerant and susceptible genotypes at reproductive stage. The breeding lines with tolerance to cold stress at the seedling and the reproductive stages identified from this study, and the SSR markers mentioned above could be useful for developing cold tolerance rice. Bangladesh Rice j. 2019, 23(2): 1-15

scholarly journals Combining QTL-seq and linkage mapping to fine map a candidate gene in qCTS6 for cold tolerance at the seedling stage in rice

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Luomiao Yang ◽  
Jingguo Wang ◽  
Zhenghong Han ◽  
Lei Lei ◽  
Hua Long Liu ◽  
...  
Keyword(s):  
Cold Stress ◽  
Cold Tolerance ◽  
Regulatory Gene ◽  
Snp Markers ◽  
Seedling Stage ◽  
Pcr Analysis ◽  
Sequencing Data ◽  
Coding Region ◽  
Rice Varieties ◽  
Major Qtl

Abstract Background Cold stress caused by low temperatures is an important factor restricting rice production. Identification of cold-tolerance genes that can stably express in cold environments is crucial for molecular rice breeding. Results In this study, we employed high-throughput quantitative trait locus sequencing (QTL-seq) analyses in a 460-individual F2:3 mapping population to identify major QTL genomic regions governing cold tolerance at the seedling stage in rice. A novel major QTL (qCTS6) controlling the survival rate (SR) under low-temperature conditions of 9°C/10 days was mapped on the 2.60-Mb interval on chromosome 6. Twenty-seven single-nucleotide polymorphism (SNP) markers were designed for the qCST6 region based on re-sequencing data, and local QTL mapping was conducted using traditional linkage analysis. Eventually, we mapped qCTS6 to a 96.6-kb region containing 13 annotated genes, of which seven predicted genes contained 13 non-synonymous SNP loci. Quantitative reverse transcription PCR analysis revealed that only Os06g0719500, an OsbZIP54 transcription factor, was strongly induced by cold stress. Haplotype analysis confirmed that +376 bp (T>A) in the OsbZIP54 coding region played a key role in regulating cold tolerance in rice. Conclusion We identified OsbZIP54 as a novel regulatory gene associated with rice cold-responsive traits, with its Dongfu-104 allele showing specific cold-induction expression serving as an important molecular variation for rice improvement. This result is expected to further exploration of the genetic mechanism of rice cold tolerance at the seedling stage and improve cold tolerance in rice varieties by marker-assisted selection.

scholarly journals Rice cold tolerance at the reproductive stage in a controlled environment

2006 ◽  
Vol 63 (3) ◽  
pp. 255-261 ◽  
Author(s):  
Renata Pereira da Cruz ◽  
Sandra Cristina Kothe Milach ◽  
Luiz Carlos Federizzi
Keyword(s):  
Cold Tolerance ◽  
Oryza Sativa L ◽  
Variable Temperature ◽  
Reproductive Stage ◽  
Spikelet Fertility ◽  
High Yield ◽  
Cold Temperatures ◽  
Cold Tolerant ◽  
Rice Genotypes ◽  
Highly Correlated

Cold tolerance of rice (Oryza sativa L.) during the reproductive stage is important to guarantee high yield under low temperature environments. Field selection, however, does not allow identification of adequate tolerance sources and limits selection of segregating lines due to variable temperature. The objective of this study was to devise methods for distinguishing rice genotypes as to their cold tolerance at the reproductive stage when evaluated under controlled temperature. The effect of cold temperatures was investigated in six rice genotypes at 17°C for varying length of time (three, five, seven and ten days) at two reproductive stages (microsporogenesis and anthesis). Cold tolerance was measured as the percentage of reduction in panicle exsertion and in spikelet fertility. Evaluating cold tolerance through the reduction in panicle exsertion did not allow for the distinction between cold tolerant from cold sensitive genotypes and, when the reduction in spikelet fertility was considered, a minimum of seven days was required to differentiate the genotypes for cold tolerance. Genotypes were more sensitive to cold at anthesis than at microsporogenesis and, as these stages were highly correlated, cold screening could be performed at anthesis only, since it is easier to determine. Rice cold tolerance at the reproductive stage may be characterized by the reduction in spikelet fertility due to cold temperature (17°C) applied for seven days at anthesis.

Identification of QTLs controlling low-temperature germinability and cold tolerance at the seedling stage in rice (Oryza Sativa L.)

Euphytica ◽  
2017 ◽  
Vol 214 (1) ◽  
Author(s):  
L. M. Yang ◽  
H. L. Liu ◽  
L. Lei ◽  
H. W. Zhao ◽  
J. G. Wang ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Low Temperature ◽  
Cold Tolerance ◽  
Oryza Sativa L ◽  
Seedling Stage

Identification of QTLs for cold tolerance at seedling stage in rice (Oryza sativa L.) using two distinct methods of cold treatment

Euphytica ◽  
2013 ◽  
Vol 195 (1) ◽  
pp. 95-104 ◽  
Author(s):  
Shaohong Zhang ◽  
Jingsheng Zheng ◽  
Bin Liu ◽  
Shaobing Peng ◽  
Hei Leung ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Cold Tolerance ◽  
Oryza Sativa L ◽  
Cold Treatment ◽  
Seedling Stage

scholarly journals GENETIC VARIATION AND RELATEDNESS AMONG HIGH YIELDING RICE VARIETIES (Oryza sativa L.) REVEALED BY RAPD MARKERS

2008 ◽  
Vol 21 (1) ◽  
pp. 07-14
Author(s):  
F. Easmin ◽  
M. S. Rahman ◽  
M. S. Islam ◽  
M. A. Samad ◽  
M. S. Alam
Keyword(s):  
Genetic Variation ◽  
Genetic Distance ◽  
Rapd Markers ◽  
Oryza Sativa L ◽  
Gene Diversity ◽  
Chain Reaction ◽  
Rice Varieties ◽  
Upgma Dendrogram ◽  
Polymerase Chain ◽  
High Level

Genetic variation is a principal concern for the plant breeders. Genetic variation and relationship among high yielding rice varieties viz. Binadhan 4, Binadhan 5, Binadhan 6, Binasail, BRRI dhan28 and BRRI dhan29 were analyzed using four decamer random primers. Polymerase Chain Reaction (PCR) amplified 22 RAPD markers, of which 18 (81.82%) were polymorphic. The proportion of polymorphic loci and the gene diversity values were 59.09% and 0.25 for the Binadhan 4; 59.09% and 0.21 for Binadhan 6; 54.55% and 0.23 for Binasail; 54.55% and 0.19 for BRRI dhan29; 50.00% and 0.19 for Binadhan 5 and 45.45% and 0.18 for BRRI dhan28, respectively. The coefficient of gene differentiation (Gst) across all loci was calculated as 0.35 reflecting the existence of high level of genetic variation among the six modern rice varieties. UPGMA dendrogram based on Nei’s genetic distance segregated the six high yielding rice varieties into two clusters: all four mutant varieties viz. Binadhan 4, Binadhan 5, Binadhan 6 and Binasail formed one cluster and two varieties of BRRI grown in boro season, BRRI dhan28 and BRRI dhan29 grouped together in another cluster. Among the mutants, two boro season varieties, developed from the same parent, Binadhan 5 and Binadhan 6 grouped together with genetic distance of 0.10. Therefore, RAPD offer a reliable method to evaluate genetic variation and relatedness among the high yielding rice varieties.DOI: http://dx.doi.org/10.3329/bjpbg.v21i1.17042

scholarly journals Cold tolerance evaluation of temperate rice (Oryza sativa L. ssp. japonica) genotypes at seedling stage

2015 ◽  
Vol 72 (1) ◽  
pp. 01-13 ◽  
Author(s):  
GABRIEL DONOSO ◽  
PATRICIA CABAS ◽  
MARIO PAREDES ◽  
VIVIANA BECERRA ◽  
MÓNICA BALZARINI
Keyword(s):  
Oryza Sativa ◽  
Cold Tolerance ◽  
Oryza Sativa L ◽  
Seedling Stage

scholarly journals Genetic diversity and population structure of core watermelon (Citrullus lanatus) genotypes using DArTseq-based SNPs

2016 ◽  
Vol 14 (3) ◽  
pp. 226-233 ◽  
Author(s):  
Xingping Yang ◽  
Runsheng Ren ◽  
Rumiana Ray ◽  
Jinhua Xu ◽  
Pingfang Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Diversity ◽  
Citrullus Lanatus ◽  
Genetic Relationships ◽  
Snp Markers ◽  
Phenotypic Characterization ◽  
Breeding Lines ◽  
I 11 ◽  
Genome Level

Watermelon [Citrullus lanatus(Thunb.) Matsum. & Nakai var.lanatus] is an economically important vegetable belonging to theCucurbitaceaefamily. Genotypes that exhibit agronomically important traits are selected for the development of elite cultivars. Understanding the genetic diversity and the genotype population structure based on molecular markers at the genome level can speed up the utilization of diverse genetic resources for varietal improvement. In the present study, we carried out an analysis of genetic diversity based on 3882 SNP markers across 37 core watermelon genotypes, including the most widely used watermelon varieties and wild watermelon. Based on the SNP genotyping data of the 37 watermelon genotypes screened, gene diversity and polymorphism information content values across chromosomes varied between 0.03–0.5 and 0.02–0.38, with averages of 0.14 and 0.13, respectively. The two wild watermelon genotypes were distinct from cultivated varieties and the remaining 35 cultivated genotypes were differentiated into three major clusters: 20 genotypes were grouped in cluster I; 11 genotypes were grouped in cluster II; three advanced breeding lines of yellow fruit flesh and genotype SW043 were grouped in cluster III. The results from neighbour-joining dendrogram, principal coordinate analysis and STRUCTURE analysis approaches were consistent, and the grouping of genotypes was generally in agreement with their origins. Here we reveal the genetic relationships among the core watermelon genotypes maintained at the Jiangsu Academy of Agricultural Sciences, China. The molecular and phenotypic characterization of the existing core watermelon genotypes, together with specific agronomic characteristics, can be utilized by researchers and breeders for future watermelon improvement.

A major QTL associated with cold tolerance at seedling stage in rice (Oryza sativa L.)

Euphytica ◽  
2007 ◽  
Vol 158 (1-2) ◽  
pp. 87-94 ◽  
Author(s):  
Qiaojun Lou ◽  
Liang Chen ◽  
Zongxiu Sun ◽  
Yongzhong Xing ◽  
Jun Li ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Cold Tolerance ◽  
Oryza Sativa L ◽  
Seedling Stage ◽  
Major Qtl

QTL analysis of cold tolerance at seedling stage in rice (Oryza sativa L.) using recombination inbred lines

2008 ◽  
Vol 48 (1) ◽  
pp. 173-179 ◽  
Author(s):  
Ling Jiang ◽  
Meimei Xun ◽  
Jiankang Wang ◽  
Jianmin Wan
Keyword(s):  
Oryza Sativa ◽  
Cold Tolerance ◽  
Qtl Analysis ◽  
Oryza Sativa L ◽  
Inbred Lines ◽  
Seedling Stage

scholarly journals Molecular characterization and morphological clustering of exotic early maturing rice (Oryza sativa L.) lines

2014 ◽  
Vol 11 (2) ◽  
pp. 233-240 ◽  
Author(s):  
MM Sarker ◽  
L Hassan ◽  
MM Rashid ◽  
S Seraj
Keyword(s):  
Oryza Sativa ◽  
Size Range ◽  
Oryza Sativa L ◽  
Gene Diversity ◽  
Allele Size ◽  
Upgma Dendrogram ◽  
Allele Size Range ◽  
Early Maturing ◽  
Positive Correlations ◽  
Simple Sequence

Characterization and variability analysis is important for the improvement of crop plant. This study aimed to evaluate the morphological and molecular variation of exotic early maturing rice (Oryza sativa L.) lines. A total of 32 exotic rice lines collected from different locations were genotyped and clustered using selected SSR markers. Based on morphological dendrogram, the lines were grouped into three clusters viz.I, II and III. Cluster I, cluster II and cluster III had 12, 11, 9 lines respectively. The results showed that the varieties were closely related belonging to the same cluster. DNA Markers namely Simple Sequence Repeats (SSR) is a useful tool for assessing genetic variations and resolving cultivar identities. Positive correlations were found between gene diversity, number of allele, the allele size range and the maximum number of repeats. Among the primers used RM147 identified more number of alleles and average PIC was 0.88. The UPGMA dendrogram based on Nei’s (1972) genetic distance grouped the 32 rice lines into three major clusters. This result indicates that the line which formed grouped together, they are less diverse. A significant level of polymorphism based on morphological and molecular levels was observed. Being grouped into three clusters C1-4-11-7P-2P-1P and IR 79201-49-1-1-1 could be utilized as potential parents for the improvement of yield in early maturing rice lines. DOI: http://dx.doi.org/10.3329/jbau.v11i2.19900 J. Bangladesh Agril. Univ. 11(2): 233-240, 2013

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