Allele Mining for the Reported Genes Governing the Yield Related Traits in a Set of Rice Germplasm Using PCR-Based Markers (original) (raw)
Related papers
Journal of Experimental Biology and Agricultural Sciences, 2020
Rice is a primary staple food for more than half of the world's population and more that 70% of Indian population. Chhattisgarh state is one of the major parts of India having richest rice biodiversity with wide genetic diversity. To make advances in rice molecular design breeding, it is important to understand the genetic background and phenotypes of germplasm lines, to know superior alleles of the breeding material. An attempt was made to identify the marker trait association for grain features with SSR markers and to identify the genetic diversity and population structure in rice germplasm lines of Chhattisgarh. In this study, 59 SSR markers were used to analyze differentiation pattern in 48 rice germplasm lines. The genetic structure showed that 48 indica lines were divided into two subgroups based on grain morphology. Sub population-1 and sub-population-2, consisted 23-23 genotypes respectively whereas two genotypes were of admixture type. Results of neighbour-joining tree (NJ tree) and PCoA analysis showed similar results of population structure analysis. GWAS analysis identified total 25 significant marker-trait associations. Of which five for grain length, four for grain length: breadth ratio, twelve for grain yield and four for thousand-grain weights were recorded. RM135 and RM201 were significantly associated with three traits viz., grain length, grain L: B ratio and total grain weight. We do hope that the results obtained through this study will be useful for future breeding programmes.
Grain size is one of the most effective characters in rice (Oryza sativa L.) yield; meanwhile it is a highly important quality trait as well. It is problematic for breeders to improve grain size in early stage of growth. Marker assisted selection (MAS) has an essential role in improvement of quantitative and qualitative traits in crops. Functional markers based on polymorphic loci within genes that directly affecting phenotypic variation improves the quality of MAS process. GS3 is a quantitative trait loci (QTL) in pericentromeric region of chromosome 3 is reported to be responsible for 80-90% of the variation in grain length and weight and the minor QTL for grain width and thickness in rice. In this investigation, the usefulness of a PCR-based SNP marker as a functional SNP in grain size was evaluated. A collection of 100 diverse rice genotypes were planted in 3 replicated lattice design and grain size characters (grain length, width and thickness) were measured. By Analysis of this SNP marker two alleles were detected. ANOVA shows a significant difference in grain size characters between these two groups of alleles. Results indicate that PCR-based SNP marker could discriminate the long and short grain; hence it could be an appropriate, simple and commodious approach for improvement of rice grain size via MAS of GS3 QTL.
Development of gene-tagged markers for quantitative trait loci underlying rice yield components
Euphytica, 2009
Higher yields of rice have always been a predominant goal in rice breeding techniques. However, the inheritances of rice yield and its components are still unknown, and no information regarding suitable alleles can be directly provided for improving the rice yield level until three major quantitative trait loci (QTLs) have been cloned and functionally characterized. These QTLs contain Gn1a for grain number per panicle and GS3 and GW2 for grain weight. It has been proven that these three genes show a potential in improving the rice yield level. However, the distribution of suitable alleles on these three loci in rice cultivars and germ plasm are yet to be elucidated, this retards the progress of the utilization of suitable alleles in rice breeding techniques to produce higher yields. In the present study, we developed a set of gene-tagged markers based on the gene mutation sites Gn1a-M1 and Gn1a-M2 for Gn1a, GW2-HapI for GW2, and GS3-PstI for GS3. The results demonstrated that these STS markers could clearly differentiate between the different alleles at each gene locus. A survey of the allele distributions of the abovementioned three genes was performed with 156 cultivars. It was observed that the 5150-Gn1a allele was absent on the Gn1a locus and only two type alleles (Ha-Gn1a and Ko-Gn1a) were present, of which 54.3% indica and 21.5% japonica cultivars contained the Ha-Gn1a allele. Two alleles (MH-GS3 and ZS-GS3) were detected on the GS3 locus, and 48.6% indica and 9.9% japonica cultivars harbored the suitable allele MH-GS3. Further, all the cultivars contained the FA-GW2 allele on GW2, whereas the WY-GW2 allele was not found. These results further suggested that some of the alleles residing in the indica subspecies have introgressed into the japonica group with a very low frequency. The gene-tagged markers developed in the present study can be directly used as a tool for marker-aided selection (MAS) in rice breeding techniques to produce higher yields.
Genetika, 2020
The present study was undertaken for allele mining of genes governing grain dimensions viz., grain length, grain width, grain thickness, grain size and grain weight. The molecular markers linked to the reported genes for these traits were used to screen 124 diverse rice genotypes. Thirty-two molecular markers used in this study produced a total of 86 alleles among 124 rice genotypes. The number of alleles ranged from 2 to 4 with an average of 2.58 alleles per locus. A dendrogram consisting of 124 rice genotypes revealed that all the genotypes can be divided into two groups. An analysis of the model-based population structure using simple sequence repeats (SSRs) covering all 12 chromosomes provided evidence of a significant population structure in the rice genotypes. The novel alleles identified in the study could be of great value for development of consumer-targeted rice varieties.
Evaluation of Agronomic Traits for Yield and Yield Components in Advance Breeding Lines of Rice
Abstract: In present work fifteen advanced lines of rice (Line-59, Line-25, Line-NPT-1, Line-161-S, Line-188, Line-186, Line-9, Line-93, Line-99, Line-184, Line-103, Line-77, Line-5, Line-18 and Line-188-S) were evaluated in the background of Bas-385 for their yield and yield attributing traits. Mean values for quantitative traits were compared according to least significant difference (LSD) statistical test. The observations were recorded in accordance with IRRI technical bulletin on morphology and varietals characteristics. Data on agronomic parameters was collected from productive tillers of three plants of each entry at appropriate stage of growth to examine variation. Among the entire yield attributing traits plant height, panicle length, primary branches, secondary branches, filled spikelets, unfilled spikelets, tillers per plant, thousand grains weight and yield per plant showed significant variability. Line-18, Line-186, Line-59, Line-103 and Line-77 proved to be best in grain yield/plant. Correlation analysis represent that yield was positively correlated with filled spikelet (0.645**P=0.01) and 1000 grains weight with primary branches (0.654* P=0.01). Range of genetic distance observed among the tested lines was (GD = 0-60%) based on SDS PAGE. The dendrogram showed that sixteen genotypes were grouped in five categories (A–E) comprising 5, 6, 2, 2 and 1 genotypes, respectively. Line-103 and Line-59 were most distantly related to each other and could be used for breeding to improve rice cultivars. To exploit their genetic potential, these genotypes can beneficially be used in the breeding programs.
International Journal of Molecular Sciences, 2019
The market success of any rice cultivar is exceedingly dependent on its grain appearance, as well as its grain yield, which define its demand by consumers as well as growers. The present study was undertaken to explore the contribution of nine major genes, qPE9~1, GW2, SLG7, GW5, GS3, GS7, GW8, GS5, and GS2, in regulating four size and weight related traits, i.e., grain length (GL), grain width (GW), grain thickness (GT), and thousand grain weight (TGW) in 204 diverse rice germplasms using Insertion/Deletion (InDel) markers. The studied germplasm displayed wide-ranging variability in the four studied traits. Except for three genes, all six genes showed considerable association with these traits with varying strengths. Whole germplasm of 204 genotypes could be categorized into three major clusters with different grain sizes and weights that could be utilized in rice breeding programs where grain appearance and weight are under consideration. The study revealed that TGW was 24.9% infl...
2022
Background: Characterization and evaluation of plant genetic resources play an important role for their utilization in the crop improvement programmes. Methods and results: This study entails the agro-morphological, cooking quality and molecular characterization of 51 genotypes / advance breeding lines of rice from Kashmir Himalayas. Signi cant variability was observed for all agromorphological and cooking quality traits among all the studied genotypes. Cluster analysis using UPGMA method divided the genotypes into two major clusters having 15 and 36 genotypes. Thirty eight genotypes screened using 24 SSR markers detected 48 alleles with 2.0 alleles per locus and an average polymorphism information content (PIC) of 0.37. High polymorphism information content (PIC) values was observed for the primers RM263 (0.67), RM159 (0.59) and RM333 (0.50). Furthermore, out of 38 SSR markers screened on 192 temperate rice germpalsm lines, R4M17 accurately differentiated indica and temperate japonica genotypes amplifying 220 bp and 169bp, respectively. Accordingly, 15 genotypes were reported as indica and 28 temperate japonica in addition to 149 genotypes as intermediate types. Conclusion: The information on marker-based diversity and performance based on cooking quality and agronomic traits helped to select the most divergent lines for crossing and also the analysis was useful to generate information on indica-japonica classi cation of our germplasm.
Effect of multiple allelic combinations of genes on regulating grain size in rice
PloS one, 2018
The grain size is one of the complex trait of rice yield controlled by a plethora of interaction of several genes in different pathways. The present study was undertaken to investigate the influence of seven known grain size regulating genes: DEP1, GS7, GS3, GW8, GL7, GS5 and GW2. A wide phenotypic variation for grain length, grain width and grain length-width ratio were observed in 89 germplasm. The correlation analysis showed a strong association among these three grain traits viz. GL, GW, GLWR and TGW which play important roles in determining the final rice grain size. Except for GW2, all six genes showed strong association with grain size traits. A total of 21 alleles were identified with an average of 2.1 allele/locus in 89 germplasm of which seven alleles were found to be favourable alleles for improving the grain size with the frequency range of 24 (26.97%) to 82 (92.13%); the largest was found in GS5 followed by GW8, GL7, DEP1, GS3 and GS7 genes. Through ANOVA, four markers ...
Journal of Genetic Resources, 2018
The economic value of different rice varieties depends on their characteristics. Knowing the genetic control of the traits will help the breeder. Genetic diversity of 85 rice genotypes evaluated using six iPBS, one IRAP, and nine ISSR markers. The studied traits included the grain area, grain length, grain width, and diameter and grain perimeter, eccentricity of brown and white. The polymorphic alleles detected by each marker (varied from 3 to 8 alleles), and an average of 5.33 alleles per locus was observed. The iPBS1854 and iPBS2242 markers with 11 bands have the highest number of bands and the iPBS2240 and iSSR55 markers with 5 bands of the least band bands. The content of the polymorphic information varied from 0.018 (iPBS2241) to 0.241 (iPBS2240) and averaged 0.195. The iPBS2240 marker with high levels of polymorphic information identified as the best marker for genetic diversity evaluation. Regression analysis was performed between phenotypic traits and molecular data for association analysis. 54 alleles were identified for evaluated traits. Of these, in a normal condition of one allele linked to the area, length, width, the eccentricity of the brown rice grain. Also, two, three, four alleles associated with the area, length and width of the white grain. In Drought stress, one single allele correlated to the area, length and width of the brown rice grain. Eight and one alleles detected for exertion from canter and perimeter of the brown rice. Also, two, four, four and eight alleles associated with the area, length, width, from canter and perimeter of the heard rice grain, respectively. Among identified alleles, ISSR1-2, iPBS2241-2, ISSR16-4, ISSR55-1, ISSR57-1, iPBS2242-2 and iPBS2240-1 associated with several traits in both normal and stress conditions The presence of common alleles is probably due to the linkage of genetic locations which control these traits or pleiotropy. We suggest that linked markers with common traits be used for breeding programs.
Introgression of Semi-Dwarf Gene in Kalanamak Rice using Marker-Assisted Selection Breeding
Current Science, 2019
Kalanamak is an important aromatic rice variety in India. Tall stature of Kalanamak causes lodging due to which its yield and other characters severely declines. Introgression of the semi-dwarfing gene (sd 1) from CSR10 was performed with the help of markerassisted breeding. Backcross-derived plants were characterized for semi-dwarf nature. Improved Kalanamak lines were analysed for the sd 1 gene and to check the presence of aroma, sensory analysis test and amplification with betaine aldehyde dehydrogenase 2 (badh 2) derived primer was performed. Improved versions of Kalanamak rice lines were either on par or superior in terms of yield, grain type and cooking quality with reduced height implicating the potentiality of marker-assisted backcross breeding for improvement of this rice variety.