Genetic Diversity and Population Structure of Myanmar Rice (Oryza sativa L.) Varieties Using DArTseq-Based SNP and SilicoDArT Markers

Thant, Aye Aye; Zaw, Hein; Kalousová, Marie; Singh, Rakesh Kumar; Lojka, Bohdan

doi:10.3390/plants10122564

Cited by 9 publications

(8 citation statements)

References 34 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…To test the association between phenotypic and genotypic data, a chi-square test of independence was performed using STAR. To display the genetic dissimilarity of tested genotypes, a weighted neighbor-joining tree was constructed in DARwin 6.0.21 [ 44 ]. To generate a dendrogram, the genotypic data was subjected to hierarchical clustering with 1000 bootstrap p -values in KDCompute 1.5.2.beta [ 45 ].…”

Section: Methodsmentioning

confidence: 99%

Identification of Drought Tolerant Rice (Oryza Sativa L.) Genotypes with Asian and African Backgrounds

Ndikuryayo

Ndayiragije

Kilasi

et al. 2023

Plants

View full text Add to dashboard Cite

Drought is among the major abiotic stresses on rice production that can cause yield losses of up to 100% under severe drought conditions. Neither of the rice varieties currently grown in Burundi can withstand very low and irregular precipitation. This study identified genotypes that have putative quantitative trait loci (QTLs) associated with drought tolerance and determined their performance in the field. Two hundred and fifteen genotypes were grown in the field under both drought and irrigated conditions. Genomic deoxyribonucleic acid (DNA) was extracted from rice leaves for further genotypic screening. The results revealed the presence of the QTLs qDTY12.1, qDTY3.1, qDTY2-2_1, and qDTY1.1 in 90%, 85%, 53%, and 22% of the evaluated genotypes, respectively. The results of the phenotypic evaluation showed a significant yield reduction due to drought stress. Yield components and other agronomic traits were also negatively affected by drought. Genotypes having high yield best linear unbiased predictions (BLUPs) with two or more major QTLs for drought tolerance, including IR 108044-B-B-B-3-B-B, IR 92522-45-3-1-4, and BRRI DHAN 55 are of great interest for breeding programs to improve the drought tolerance of lines or varieties with other preferred traits.

show abstract

Section: Methodsmentioning

confidence: 99%

Identification of Drought Tolerant Rice (Oryza Sativa L.) Genotypes with Asian and African Backgrounds

Ndikuryayo

Ndayiragije

Kilasi

et al. 2023

Plants

View full text Add to dashboard Cite

show abstract

“…For increasing grain output via breeding, it is important to recognize the species’ variability, the nature of character associations, and the involvement of various traits [ 13 , 14 ]. The growing demand for rice necessitates the development of outstanding genotypes that can thrive in an assortment of environments [ 15 , 16 ]. Grain yield (GY) is a multifaceted attribute that is impacted by an arrangement of genes, the environment in which they develop, and the degree and types of diversity in genotypes [ 17 ].…”

Section: Introductionmentioning

confidence: 99%

Genetic Variability, Character Association, and Path Coefficient Analysis in Transplant Aman Rice Genotypes

Faysal

Ali

Azam

et al. 2022

Plants

View full text Add to dashboard Cite

A field experiment was carried out with 20 genotypes of Transplant Aman (T. Aman) rice at the Department of Genetics and Plant Breeding, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Salna, Gazipur-1706, Bangladesh. The study was performed to evaluate the genetic deviation, trait association, and path coefficient (PC) based on grain yield (GY) and different yield-contributing agronomic characters. Variance analysis displayed extensive traits-wise variations across accessions, indicating variability and the opportunity for genetic selection for desirable traits. The high mean, range, and genotypic variances observed for most of the characters indicated a wide range of variation for these traits. All the characters indicated the minimum influence of environment on the expression of the trait and genetic factors had a significant role in the expressivity of these characters. High heritability in broad sense (h2b) and high to moderate genetic advance in percent of the mean (GAPM) were recorded for all the characters except for panicle length (PL). Based on mean, range, and all genetic parameters, the selection of all the traits except for PL would contribute to the development of T. Aman rice genotypes. A correlation study revealed that selection based on plant height (PH), number of effective tillers per hill (NET), PL, number of filled spikelets per panicle (NFS), flag leaf length (FLL), spikelet sterility (SS) percentage, and harvest index (HI) would be effective for increasing the GY of rice. Genotypic correction with grain yield (GCGY), PC and principal component analysis (PCA) revealed that direct selection of NFS, HI, SS%, and FLL would be effective for improving the GY of rice in future breeding programs.

show abstract

“…The leaf samples from TOS6454/FARO44 and TOS6454/FARO60 populations were sent to Diversity Array Technology in Australia for genotyping using the DArTseq approach (http://www.diversityarrays.com/services/dartseq/) (Table S1). The details of DArTseq methodology and its use in rice are well described (Kilian et al., 2012; Thant et al., 2021). Briefly, in the DArTseq approach, whole‐genome scans are performed using a combination of DArT complexity reduction method and next‐generation sequencing platform.…”

Section: Methodsmentioning

confidence: 99%

qSUB2: A novel QTL with positive epistasis with SUB1 locus enhances submergence tolerance in rice

et al. 2023

View full text Add to dashboard Cite

Climate change is expected to significantly increase submergence stress of lowland rice (Oryza sativa) production in Africa. There is a need to further improve the ability of SUB1 gene to tolerate submergence stress. Genetic control of submergence tolerance was studied in a moderately tolerant to submergence African rice landrace “TOS6454.” Three mapping populations with a total of 1182 lines were developed by crossing TOS6454 with three popular rice varieties of West Africa that are high‐yielding but submergence susceptible, that is, FARO44, FARO52, and FARO60. The screening for submergence was conducted at the Africa Rice Center (AfricaRice) station in Ibadan, Nigeria during 2016–2018. The three mapping populations were genotyped with single nucleotide polymorphic markers either on the Kompetitive allele specific PCR or the DArTseq platforms. Quantitative trait locus (QTL) analysis revealed five different QTLs on chromosomes 1, 2, 3, 4, and 9. The QTLs on chromosomes 2 (qSUB2) and 9 (qSUB9) had consistent large effects and the tolerance alleles were contributed by TOS6454. The QTL on chromosome 9 (qSUB9) had a large effect on submergence tolerance in all three mapping populations. This QTL had a highest logarithm of odds (LOD) score of 30.46 and explained as much as 27.7% phenotypic variation (R2), with an additive effect of up to 9.39. The QTL on chromosome 2 (qSUB2) had a highest LOD score of 10.78 and explained up to 10.8% R2 for this trait. Furthermore, qSUB2 had positive epistasis with qSUB9 which further increased submergence tolerance. A total of 57 lines carrying both qSUB2 and qSUB9 alleles were superior to all other lines in submergence tolerance. qSUB9 co‐segregated with ART5 a marker for the SUB1 gene; thus, it is suggested that qSUB9 is the same as the well‐known SUB1 gene. Pyramiding qSUB2 with the SUB1 gene locus is expected to further improve submergence tolerance in elite rice varieties.

show abstract

Genetic Diversity and Population Structure of Myanmar Rice (Oryza sativa L.) Varieties Using DArTseq-Based SNP and SilicoDArT Markers

Cited by 9 publications

References 34 publications

Identification of Drought Tolerant Rice (Oryza Sativa L.) Genotypes with Asian and African Backgrounds

Identification of Drought Tolerant Rice (Oryza Sativa L.) Genotypes with Asian and African Backgrounds

Genetic Variability, Character Association, and Path Coefficient Analysis in Transplant Aman Rice Genotypes

qSUB2: A novel QTL with positive epistasis with SUB1 locus enhances submergence tolerance in rice

Contact Info

Product

Resources

About