scholarly journals Fine-mapping of qTGW2, a quantitative trait locus for grain weight in rice (Oryza sativa L.)

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8679 ◽  
Author(s):  
Hui Zhang ◽  
Yu-Jun Zhu ◽  
An-Dong Zhu ◽  
Ye-Yang Fan ◽  
Ting-Xu Huang ◽  
...  
Keyword(s):  
Qtl Analysis ◽  
Quantitative Trait ◽  
Oryza Sativa L ◽  
Grain Weight ◽  
Width Ratio ◽  
Isogenic Line ◽  
Rice Varieties ◽  
Grain Length ◽  
Major Qtls ◽  
Length Width

Background Grain weight is a grain yield component, which is an integrated index of grain length, width and thickness. They are controlled by a large number of quantitative trait loci (QTLs). Besides major QTLs, minor QTLs play an essential role. In our previous studies, QTL analysis for grain length and width was performed using a recombinant inbred line population derived from rice cross TQ/IRBB lines. Two major QTLs were detected, which were located in proximity to GS3 and GW5 that have been cloned. In the present study, QTLs for grain weight and shape were identified using rice populations that were homozygous at GS3 and GW5. Method Nine populations derived from the indica rice cross TQ/IRBB52 were used. An F10:11population named W1, consisting of 250 families and covering 16 segregating regions, was developed from one residual heterozygote (RH) in the F7generation of Teqing/IRBB52. Three near isogenic line (NIL)-F2 populations, ZH1, ZH2 and ZH3 that comprised 205, 239 and 234 plants, respectively, were derived from three RHs in F10:11. They segregated the target QTL region in an isogenic background. Two NIL populations, HY2 and HY3, were respectively produced from homozygous progeny of the ZH2 and ZH3 populations. Three other NIL-F2 populations, Z1, Z2 and Z3, were established using three RHs having smaller heterozygous segments. QTL analysis for 1000-grain weight (TGW), grain length (GL), grain width (GW), and length/width ratio (LWR) was conducted using QTL IciMapping and SAS procedure with GLM model. Result A total of 27 QTLs distributed on 12 chromosomes were identified. One QTL cluster, qTGW2/qGL2/qGW2 located in the terminal region of chromosome 2, were selected for further analysis. Two linked QTLs were separated in region Tw31911−RM266. qGL2 was located in Tw31911−Tw32437 and mainly controlled GL and GW. The effects were larger on GL than on GW and the allelic directions were opposite. qTGW2 was located in Tw35293−RM266 and affected TGW, GL and GW with the same allelic direction. Finally, qTGW2 was delimited within a 103-kb region flanked by Tw35293 and Tw35395. Conclusion qTGW2 with significant effects on TGW, GL and GW was validated and fine-mapped using NIL and NIL-F2 populations. These results provide a basis for map-based cloning of qTGW2 and utilization of qTGW2 in the breeding of high-yielding rice varieties.

scholarly journals Dissection of three quantitative trait loci for grain size on the long arm of chromosome 10 in rice (Oryza sativa L.)

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6966 ◽  
Author(s):  
Yu-Jun Zhu ◽  
Zhi-Chao Sun ◽  
Xiao-Jun Niu ◽  
Jie-Zheng Ying ◽  
Ye-Yang Fan ◽  
...  
Keyword(s):  
Grain Size ◽  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Oryza Sativa L ◽  
Grain Weight ◽  
The Other ◽  
Isogenic Line ◽  
Chromosome 10 ◽  
High Effect ◽  
Trait Loci

Background Thousand grain weight is a key component of grain yield in rice, and a trait closely related to grain length (GL) and grain width (GW) that are important traits for grain quality. Causal genes for 16 quantitative trait loci (QTL) affecting these traits have been cloned, but more QTL remain to be characterized for establishing a genetic regulating network. A QTL controlling grain size in rice, qGS10, was previously mapped in the interval RM6100–RM228 on chromosome 10. This study aimed to delimitate this QTL to a more precise location. Method A total of 12 populations were used. The ZC9 population comprised 203 S1:2 families derived from a residual heterozygous (RH) plant in the F9 generation of the indica rice cross Teqing (TQ)/IRBB52, segregating the upper region of RM6100–RM228 and three more regions on chromosomes 1, 9, and 11. The Ti52-1 population comprised 171 S1 plants derived from one RH plant in F7 of TQ/IRBB52, segregating a single interval that was in the lower portion of RM6100–RM228. The other ten populations were all derived from Ti52-1, including five S1 populations with sequential segregating regions covering the target region and five near isogenic line (NIL) populations maintaining the same segregating pattern. QTL analysis for 1,000-grain weight, GL, and GW was performed using QTL IciMapping and SAS procedure GLM. Result Three QTL were separated in the original qGS10 region. The qGL10.1 was located in the upper region RM6704–RM3773, shown to affect GL only. The qGS10.1 was located within a 207.1-kb interval flanked by InDel markers Te20811 and Te21018, having a stable and relatively high effect on all the three traits analyzed. The qGS10.2 was located within a 1.2-Mb interval flanked by simple sequence repeat markers RM3123 and RM6673. This QTL also affected all the three traits but the effect was inconsistent across different experiments. QTL for grain size were also detected in all the other three segregating regions. Conclusion Three QTL for grain size that were tightly linked on the long arm of chromosome 10 of rice were separated using NIL populations with sequential segregating regions. One of them, qGS10.1, had a stable and relatively high effect on grain weight, GL, and GW, providing a good candidate for gene cloning. Another QTL, qGS10.2, had a significant effect on all the three traits but the effect was inconsistent across different experiments, providing an example of genotype-by-environmental interaction.

scholarly journals Genetic divergence analysis in basmati rice genotypes (Oryza sativa L.) for agro-morphological and quality traits using multivariate approach

2021 ◽  
Vol 58 (1) ◽  
pp. 1-7
Author(s):  
Vinod Kumar ◽  
Dhirendra Singh
Keyword(s):  
Genetic Divergence ◽  
Amylose Content ◽  
Oryza Sativa L ◽  
Grain Weight ◽  
Basmati Rice ◽  
Quality Traits ◽  
Grain Length ◽  
Cluster Distance ◽  
Rice Genotypes ◽  
1000 Grain Weight

Genetic diversity of 30 basmati rice genotypes was analysed based on nine agro-morphological and six quality traits. The results of the principal component analysis showed that the first six principal components explained 89.16% of the total variation in the experimental material. These 30 basmati genotypes were grouped into six clusters which indicated the presence of sufficient diversity among the tested genotypes. Cluster I and cluster III was found to be the largest comprising of 10 genotypes each followed by cluster II having seven genotypes. The highest average intra-cluster distance was observed in cluster III. Highest inter-cluster distance (D2) was observed between clusters III and VI followed by clusters III and V, III and IV & clusters II and III. Cluster II showed high mean value for grain yield per plant, 1000 grain weight, and grain length. The characters viz., amylose content, grain length after cooking, spikelet per panicle, grain width, grain length and 1000 grain weight contributed maximum towards total genetic divergence, suggest their suitability of selection.

scholarly journals Identification of Grain Size-Related QTLs in Korean japonica Rice Using Genome Resequencing and High-Throughput Image Analysis

Agriculture ◽  
2022 ◽  
Vol 12 (1) ◽  
pp. 51
Author(s):  
Yunji Shin ◽  
Yong Jae Won ◽  
Chaewon Lee ◽  
Kyeong-Seong Cheon ◽  
Hyoja Oh ◽  
...  
Keyword(s):  
Grain Size ◽  
Image Analysis ◽  
High Throughput ◽  
Width Ratio ◽  
Japonica Rice ◽  
Multiple Traits ◽  
Genome Resequencing ◽  
Rice Varieties ◽  
Grain Length ◽  
Six Traits

Grain size is a key factor influencing the grain yield in rice. To identify the as-yet-unknown genes regulating grain size in Korean japonica rice, we developed a recombinant inbred line population (n = 162) from a cross between Odae (large-grain) and Joun (small-grain), and measured six traits including the thousand-grain weights of unhulled and hulled seeds, grain area, grain length, grain width and grain length-to-width ratio using high-throughput image analysis at the F8 and F9 generations. A genetic map was constructed using 248 kompetitive allele-specific PCR (KASP) markers that were polymorphic between the parental genotypes, and 29 QTLs affecting the six traits were identified, of which 15 were stable in both F8 and F9 generations. Notably, three QTL clusters affecting multiple traits were detected on chromosomes 6, 7 and 11. We analyzed whole-genome resequencing data of Odae and Joun, and selected candidate genes for the stable QTLs in the identified clusters that have high- or moderate-impact variations between Odae and Joun and encode proteins the families of which have been reported to be related to grain size regulation. These results will facilitate the identification of genes underlying the QTLs and promote molecular breeding of high-yielding Korean japonica rice varieties.

scholarly journals Ageing Effects, Generation Means, and Path Coefficient Analyses on High Kernel Elongation in Mahsuri Mutan and Basmati 370 Rice Populations

2021 ◽  
Vol 2021 ◽  
pp. 1-20
Author(s):  
Anna Arina Bt Ab. Halim ◽  
Mohd Y. Rafii ◽  
Mohamad B. Osman ◽  
Yusuff Oladosu ◽  
Samuel C. Chukwu
Keyword(s):  
Quantitative Traits ◽  
External Factor ◽  
Gene Interaction ◽  
Width Ratio ◽  
Path Coefficient ◽  
Rice Varieties ◽  
Generation Means ◽  
Ageing Effects ◽  
Length Width ◽  
Two Populations

High kernel elongation (HKE) is one of the high-quality characteristics in rice. The objectives of this study were to determine the effects of ageing treatments, gene actions, and inheritance pattern of kernel elongation on cooking quality in two populations of rice and determine the path of influence and contribution of other traits to kernel elongation in rice. Two rice populations derived from crosses between MR219 × Mahsuri Mutan and MR219 × Basmati 370 were used. The breeding materials included two F1 progenies from the two populations, and their respective parents were grown in four different batches at a week interval to synchronize the flowering between the female and male plants. Scaling tests and generation means analysis were carried out to determine ageing effects and estimate additive-dominance gene action and epistasis. The estimation of gene interaction was based on quantitative traits. Path coefficient analysis was done using SAS software version 9.4 to determine the path of influence (direct or indirect) of six quantitative traits on HKE. Results obtained showed that nonallelic gene interaction was observed in all traits. The results before ageing and after ageing showed significant differences in all traits, while the gene interaction changed after ageing. The HKE value improved after ageing, suggesting that ageing is an external factor that could influence gene expression. The epistasis effect for HKE obtained from the cross Mahsuri Mutan × MR219 showed duplicate epistasis while that obtained from a cross between Basmati 370 × MR219 showed complimentary epistasis. Besides, the heritability of HKE was higher in Basmati 370 × MR219 compared to that obtained in Mahsuri Mutan × MR219. The path analysis showed that the cooked grain length and length-width ratio positively significantly affected HKE. It was concluded that ageing treatment is an external factor that could improve the expression of HKE. The findings from this study would be useful to breeders in the selection and development of new specialty (HKE) rice varieties.

scholarly journals Mapping of qTGW1.1, a Quantitative Trait Locus for 1000-Grain Weight in Rice (Oryza sativa L.)

Rice Science ◽  
2015 ◽  
Vol 22 (1) ◽  
pp. 9-15 ◽  
Author(s):  
ZHANG Hong-wei ◽  
CHEN Yu-yu ◽  
CHEN Jun-yu ◽  
ZHU Yu-jun ◽  
HUANG De-run ◽  
...  
Keyword(s):  
Quantitative Trait Locus ◽  
Oryza Sativa ◽  
Quantitative Trait ◽  
Oryza Sativa L ◽  
Grain Weight ◽  
Trait Locus ◽  
1000 Grain Weight

scholarly journals GENETIC VARIABILITY FOR GRAIN QUALITY TRAITS IN AROMATIC RICE (Oryza sativa L)

2011 ◽  
Vol 24 (2) ◽  
pp. 19-24
Author(s):  
Kaniz Fatema ◽  
M. G. Rasul ◽  
M. A. K. Mian ◽  
M. M. Rahman
Keyword(s):  
Genetic Variability ◽  
Amylose Content ◽  
Oryza Sativa L ◽  
Grain Weight ◽  
Aromatic Rice ◽  
Thousand Grain Weight ◽  
Grain Length ◽  
Gel Consistency ◽  
Rice Genotypes ◽  
1000 Grain Weight

Forty five aromatic rice genotypes were evaluated to assess the genetic variability and diversity on the basis of nine characters. Significant variations were observed among the genotypes for all the characters (grain breadth (mm), grain length (mm), grain L/B ratio, gelatinization temperature (score), gel consistency (mm), amylose content (%), protein content (%), 1000 grain weight (g) and grain yield per plant (g)) studied. High GCV, PCV, heritability and GA as observed in amylose content, grain length average and L/B ratio suggested that these three characters could be transmitted to the progeny. Multivariate analysis revealed that 45 genotypes were grouped into six clusters. There were marked variations in intra-cluster distances, which ranged from 0.482 to 7.851. The highest intra cluster mean for five traits (amylose content, width average, L/B ratio, length average, 1000 grain weight) was obtained from cluster I constituted 10 genotypes. Thousand grain weight and amylose content have been found to contribute maximum towards genetic diversity in 45 genotypes of aromatic rice.DOI: http://dx.doi.org/10.3329/bjpbg.v24i2.17002

Sign in / Sign up

Export Citation Format

Share Document