Association Mapping of Thousand Grain Weight using SSR and SNP Markers in Rice (Oryza sativa L.) Across Six Environments

AbstractThousand grain weight (TGW) is an important determinant of rice yield, and correlates with grain size, plumpness and grain number per panicle. In rice, there are fewer association mapping studies relating grain weight traits using both SSR and SNP markers. In this study, in order to find robust SSR markers associated with TGW trait and mine elite accessions in rice, we investigated the TGW trait across six environments using a natural population consisted of 462 accessions, and then performed association mapping using both SSR and SNP markers. Using the six datasets from the six environments and their best linear unbiased estimator, we identified eight TGW associated SSR markers, with three environmentally stable and one newly found, on five chromosomes. The associated markers have genetic effect from 3.44% to 20.84%, and two of them carry stable elite allele with positive effect across different environments. Candidate interval association mapping using re-sequencing derived SNP/InDel markers further confirms the TGW-SSR association, and also suggests that 3 TGW-SSR associations were high confident in intervals of size from 176 to 603 kb. These results not only shed more lights on the genetics of TGW trait, but also suggest that the multi-allelic SSR markers should be used as an alternative power tool in gene or QTL mapping.

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Character association and path analysis in bacterial blight resistance genes pyramided segregating populations of rice (Oryza sativa L.)

Genetika ◽

10.2298/gensr1801011g ◽

2018 ◽

Vol 50 (1) ◽

pp. 11-20

Author(s):

Ponnaiah Govintharaj ◽

Swaminathan Manonmani ◽

Sabariappan Robin

Keyword(s):

Resistance Genes ◽

Bacterial Blight ◽

Oryza Sativa L ◽

Research Work ◽

Grain Weight ◽

Blight Resistance ◽

Exploratory Research ◽

Bacterial Blight Resistance ◽

Thousand Grain Weight ◽

Character Association

An exploratory research work was conducted to study the character association and their direct and indirect effects on grain yield in three bacterial blight resistance genes introgressed segregating populations (F2) in rice. Data for yield and five other traits which were component of yield were recorded in 449 F2 individuals in all three crosses. Thousand grain weight was highly correlated with single plant yield in (r=0.95**, p<0.01) CB 174 R ? IRBB 60> (r=0.48**, p<0.01) CB 87 R ? IRBB 60> (r=0.44**, p<0.01) TNAU CMS 2B ? IRBB 60. Thousand grain weight was exhibited important yield determining component for CB 174 R ? IRBB 60 (0.92) and CB 87 R ? IRBB 60 (0.45), and panicle length for (0.39) TNAU CMS 2B ? IRBB 60 by direct effect. The genetic information derived from our study could be useful to select potential segregating individual among the F2 population for future rice breeding program.

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Association Mapping for Important Agronomic Traits in Core Collection of Rice (Oryza sativa L.) with SSR Markers

PLoS ONE ◽

10.1371/journal.pone.0111508 ◽

2014 ◽

Vol 9 (10) ◽

pp. e111508 ◽

Cited By ~ 33

Author(s):

Peng Zhang ◽

Xiangdong Liu ◽

Hanhua Tong ◽

Yonggen Lu ◽

Jinquan Li

Keyword(s):

Oryza Sativa ◽

Association Mapping ◽

Ssr Markers ◽

Core Collection ◽

Agronomic Traits ◽

Oryza Sativa L

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

Bangladesh Journal of Plant Breeding and Genetics ◽

10.3329/bjpbg.v24i2.17002 ◽

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

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Association Mapping for Important Agronomic Traits in Core Collection of Rice (Oryza sativa L.) with SSR Markers

International Journal of Current Microbiology and Applied Sciences ◽

10.20546/ijcmas.2020.904.374 ◽

2020 ◽

Vol 9 (4) ◽

pp. 3216-3224

Author(s):

Ritu R. Saxena ◽

Sujit Roy ◽

Suman Rawte ◽

Parmeshwar K. Sahu ◽

Ravi R. Saxena ◽

...

Keyword(s):

Oryza Sativa ◽

Association Mapping ◽

Ssr Markers ◽

Core Collection ◽

Agronomic Traits ◽

Oryza Sativa L

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Genetic Variability And Character Associations In Irrigated Rice (Oryza Sativa L)

Bangladesh Journal of Plant Breeding and Genetics ◽

10.3329/bjpbg.v23i2.9321 ◽

1970 ◽

Vol 23 (2) ◽

pp. 23-28 ◽

Cited By ~ 3

Author(s):

S Ghosal ◽

PL Biswas ◽

M Khatun ◽

S Khatun

Keyword(s):

Oryza Sativa ◽

Genetic Variability ◽

Grain Yield ◽

Oryza Sativa L ◽

Grain Weight ◽

Path Coefficient ◽

Genetic Advance ◽

Thousand Grain Weight ◽

Growth Duration ◽

Irrigated Rice

Eighteen advanced breeding lines were evaluated for yield and yield contributing characters to observe their variability, associations and direct and indirect effect on yield during Boro season, 2009. All the tested characters showed significant variation. Effective tillers/m2 and spikelet sterility (%) had high genotypic variance, high heritability, high genetic advance and high genotypic coefficient of variation. Effective tillers/m2, panicle length (cm), thousand grain weight (g) and growth duration (days) showed significant positive association with grain yield. Path coefficient analysis also revealed that effective tillers/m2, thousand grain weight (g) and growth duration (days) had higher direct effects on yield (t/ha). All together with the genetic variability, correlation and path analysis revealed that effective tillers/m2, thousand grain weight (g) and growth duration (days) are the most important yield components in rice. Therefore, from the present study it could be suggested that emphasize should be given on these characters for the selection of genotypes for higher grain yield in irrigated rice. Keywords: Rice (Oryza sativa L.); GCV; PCV; heritability; genetic advance; correlationDOI: http://dx.doi.org/10.3329/bjpbg.v23i2.9321 Bangladesh J. Pl. Breed. Genet., 23(2): 23-27, 2010

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Choice of parents for developing two line hybrids in rice (Oryza sativa L.)

Journal of Applied and Natural Science ◽

10.31018/jans.v9i4.1487 ◽

2017 ◽

Vol 9 (4) ◽

pp. 2047-2054

Author(s):

V. Karpagam ◽

R. Kalaiyarasi

Keyword(s):

Oryza Sativa L ◽

Grain Weight ◽

Hybrid Breeding ◽

Hybrid Seed Production ◽

Thousand Grain Weight ◽

Male Sterile ◽

Cent Increase ◽

Additive Gene ◽

Line Breeding ◽

Low X

An investigation was carried out to evaluate two line hybrids in rice for yield traits. Four TGMS lines and eleven testers were crossed in line x Tester design. Greater proportion of sca variance was observed for all the characters which revealed that preponderance of non- additive gene action governing traits concerned and selection procedures based on the accumulation of additive effects would be successful in improving these traits. The line TS09 24 and testers viz., T 2006, KDML 105, Improved white ponni and BPT 5204 were found to be good combiners for the yield and yield components. The best hybrids based on sca value, TNAU 27S x Improved white ponni was derived from low x low combiners for thousand grain weight and TS 29 X ADT 38 for the number of filled grains per panicle spikelet fertility. The best performing hybrid TS 29 x KDML 105 produced 54.25g of grain yield per plant in 128 days which was 92.89 and 85.47 per cent increase over the standard checks CORH 3 and Improved white ponni respectively. This hybrid also recorded 27.32 and 64.30 per cent increase CORH 3 and Improved white ponni for thousand grain weight. Hence, the two line hybrid breeding system, utilizing thermo sensitive genic male sterility is economically feasible as well as viable alternative to cytoplasmic male sterile (CMS) based three line breeding due to much simplified hybrid seed production.

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Genomic dissection of plant development and its impact on thousand grain weight in barley through nested association mapping

Journal of Experimental Botany ◽

10.1093/jxb/erw070 ◽

2016 ◽

Vol 67 (8) ◽

pp. 2507-2518 ◽

Cited By ~ 46

Author(s):

Andreas Maurer ◽

Vera Draba ◽

Klaus Pillen

Keyword(s):

Association Mapping ◽

Plant Development ◽

Grain Weight ◽

Thousand Grain Weight ◽

Nested Association Mapping

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Assessment of the Origin and Diversity of Croatian Common Bean Germplasm Using Phaseolin Type, SSR and SNP Markers and Morphological Traits

Plants ◽

10.3390/plants10040665 ◽

2021 ◽

Vol 10 (4) ◽

pp. 665

Author(s):

Monika Vidak ◽

Zlatko Šatović ◽

Zlatko Liber ◽

Martina Grdiša ◽

Jerko Gunjača ◽

...

Keyword(s):

Population Structure ◽

Common Bean ◽

Ssr Markers ◽

Morphological Characterization ◽

Snp Markers ◽

Human Consumption ◽

Clustering Methods ◽

Model Based ◽

True Type ◽

Ssr And Snp Markers

Landraces represent valuable genetic resources for breeding programmes to produce high-yielding varieties adapted to stressful environmental conditions. Although the common bean (Phaseolus vulgaris L.) is an economically important food legume for direct human consumption worldwide, common bean production in Croatia is based almost exclusively on landraces and there is no common bean breeding program. Information on phaseolin type and results of population structure and genetic diversity obtained by analysis of SSR and SNP markers, in combination with the morphological characterization of 174 accessions of 10 common bean landraces (morphotypes), enabled thorough classification of accessions. The accessions were classified into phaseolin type H1 (“S”) of Mesoamerican origin and phaseolin types H2 (“H” or “C”) and H3 (“T”) of Andean origin. By applying distance- and model-based clustering methods to SSR markers, the accessions were classified into two clusters at K = 2 separating the accessions according to the centres of origin, while at K = 3, the accessions of Andean origin were further classified into two clusters of accessions that differed in phaseolin type (H2 and H3). Using SNP markers, model-based analysis of population structure was performed, the results of which were consistent with those of SSR markers. In addition, 122 accessions were assigned to 14 newly formed true-type morphogenetic groups derived from three different domestication events: (1) Mesoamerican (H1A) (“Biser”, “Kukuruzar”, “Tetovac”, “Trešnjevac”), (2) Andean—indeterminate type (H2B1) (“Dan noć”, “Sivi”, “Puter”, ”Sivi prošarani”, “Trešnjevac”) and (3) Andean—determinate type (H3B2) (“Bijeli”, “Dan noć”, “Puter”, “Trešnjevac”, “Zelenčec”). The rest of the accessions could represent putative hybrids between morphogenetic groups. The differences between the true-type groups of accessions were further analysed based on nine quantitative traits, and the subsets of traits that best distinguish among centres of origin (A: Mesoamerican, B: Andean) and genetic groups (H1A, H2B1, H3B2) were proposed.

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