Researches:
Article title: Mining of Cloned Disease Resistance Gene Homologs (CDRHs) in Brassica Species and Arabidopsis thaliana
Authors: Aldrin Y. Cantila, Ting X. Neik, Soodeh Tirnaz, William J.W. Thomas, Philipp E. Bayer, David Edwards, Jacqueline Batley
Publication title: Biology 11(6):821, 2022
Abstract:
Various diseases severely affect Brassica crops, leading to significant global yield losses and a reduction in crop quality. In this study, we used the complete protein sequences of 49 cloned resistance genes (R genes) that confer resistance to fungal and bacterial diseases known to impact species in the Brassicaceae family. Homology searches were carried out across Brassica napus, B. rapa, B. oleracea, B. nigra, B. juncea, B. carinata and Arabidopsis thaliana genomes. In total, 660 cloned disease R gene homologs (CDRHs) were identified across the seven species, including 431 resistance gene analogs (RGAs) (248 nucleotide binding site-leucine rich repeats (NLRs), 150 receptor-like protein kinases (RLKs) and 33 receptor-like proteins (RLPs)) and 229 non-RGAs. Based on the position and distribution of specific homologs in each of the species, we observed a total of 87 CDRH clusters composed of 36 NLR, 16 RLK and 3 RLP homogeneous clusters and 32 heterogeneous clusters. The CDRHs detected consistently across the seven species are candidates that can be investigated for broad-spectrum resistance, potentially providing resistance to multiple pathogens. The R genes identified in this study provide a novel resource for the future functional analysis and gene cloning of Brassicaceae R genes towards crop improvement.
Full text link https://tinyurl.com/ym2f3ck9
Article title: Advancing designer crops for climate resilience through an integrated genomics approach
Authors: Nur Shuhadah Mohd Saad, Ting Xiang Neik, William J.W. Thomas, Junrey C. Amas, Aldrin Y. Cantila, Ryan J. Craig, David Edwards, Jacqueline Batley
Publication title: Current Opinion in Plant Biology 67, 2022
Abstract:
Climate change and exponential population growth are exposing an immediate need for developing future crops that are highly resilient and adaptable to changing environments to maintain global food security in the next decade. Rigorous selection from long domestication history has rendered cultivated crops genetically disadvantaged, raising concerns in their ability to adapt to these new challenges and limiting their usefulness in breeding programmes. As a result, future crop improvement efforts must rely on integrating various genomic strategies ranging from high-throughput sequencing to machine learning, in order to exploit germplasm diversity and overcome bottlenecks created by domestication, expansive multi-dimensional phenotypes, arduous breeding processes, complex traits and big data.
Full text available upon request to the author/s
Article title: Predicting Cloned Disease Resistance Gene Homologs (CDRHs) in Radish, Underutilised Oilseeds, and Wild Brassicaceae Species
Authors: Aldrin Y. Cantila, William J.W. Thomas, Philipp E. Bayer, David Edwards, Jacqueline Batley
Publication title: Plants 11(22):3010, 2022
Abstract:
Brassicaceae crops, including Brassica, Camelina and Raphanus species, are among the most economically important crops globally; however, their production is affected by several diseases. To predict cloned disease resistance (R) gene homologs (CDRHs), we used the protein sequences of 49 cloned R genes against fungal and bacterial diseases in Brassicaceae species. In this study, using 20 Brassicaceae genomes (17 wild and 3 domesticated species), 3172 resistance gene analogs (RGAs) (2062 nucleotide binding-site leucine-rich repeats (NLRs), 497 receptor-like protein kinases (RLKs) and 613 receptor-like proteins (RLPs)) were identified. CDRH clusters were also observed in Arabis alpina, Camelina sativa and Cardamine hirsuta with assigned chromosomes, consisting of 62 homogeneous (38 NLR, 17 RLK and 7 RLP clusters) and 10 heterogeneous RGA clusters. This study highlights the prevalence of CDRHs in the wild relatives of the Brassicaceae family, which may lay the foundation for rapid identification of functional genes and genomics-assisted breeding to develop improved disease-resistant Brassicaceae crop cultivars.
Full text link https://tinyurl.com/57mzktea
Article title: The Impact of Genomics in Identifying Blackleg Disease Resistance Genes in Canola
Authors: William J.W. Thomas, Junrey C. Amas, Tingting Wu, Aldrin Y. Cantila, Linh B. Ton, Jacqueline Batley
Publication title: Next-generation Sequencing and Agriculture 12(24):24, 2022
Abstract:
Blackleg disease, caused by the fungal pathogen Leptosphaeria maculans, poses a serious threat to canola (Brassica napus) production worldwide. However, the deployment of resistance (R) genes is a cost-effective, reliable and sustainable measure for managing the disease. This chapter reports the recent advances in sequencing and genomics, and how they have been vital for the rapid identification of R genes responsible for conferring blackleg resistance in canola. Promising new genomic technologies which may accelerate future identification efforts are also discussed.
Full text available upon request to the author/s.
Article title: In silico integration of disease resistance QTL, genes and markers with the Brassica juncea physical map
Authors: Fabian Inturrisi, Philipp E. Bayer, Aldrin Y. Cantila, Soodeh Tirnaz, David Edwards, Jacqueline Batley
Publication title: Molecular Breeding 42(7):37, 2022
Abstract:
Brassica juncea (AABB), Indian mustard, is a source of disease resistance genes for a wide range of pathogens. The availability of reference genome sequences for B. juncea has made it possible to characterise the genomic structure and distribution of these disease resistance genes. Potentially functional disease resistance genes can be identified by co-localization with genetically mapped disease resistance quantitative trait loci (QTL). Here we identify and characterise disease resistance gene analogs (RGAs), including nucleotide-binding site–leucine-rich repeat (NLR), receptor-like kinase (RLK) and receptor-like protein (RLP) classes, and investigate their association with disease resistance QTL intervals. The molecular genetic marker sequences for four white rust (Albugo candida) disease resistance QTL, six blackleg (Leptosphaeria maculans) disease resistance QTL and BjCHI1, a gene cloned from B. juncea for hypocotyl rot disease, were extracted from previously published studies and used to compare with candidate RGAs. Our results highlight the complications for the identification of functional resistance genes, including the duplicated appearance of genetic markers for several resistance loci, including Ac2(t), AcB1-A4.1, AcB1-A5.1, Rlm6 and PhR2 in both the A and B genomes, due to the presence of homoeologous regions. Furthermore, the white rust loci, Ac2(t) and AcB1-A4.1, mapped to the same position on chromosome A04 and may be different alleles of the same gene. Despite these challenges, a total of nine candidate genomic regions hosting 14 RLPs, 28 NLRs and 115 RLKs were identified. This study facilitates the mapping and cloning of functional resistance genes for applications in crop improvement programs.
Full text available upon request to the author/s.
Article title: Recent Findings Unravel Genes and Genetic Factors Underlying Leptosphaeria maculans Resistance in Brassica napus and Its Relatives
Authors: Aldrin Y. Cantila, Nur Shuhadah Mohd Saad, Junrey C. Amas, David Edwards, Jacqueline Batley
Publication title: International Journal of Molecular Sciences 22(1):313, 2020
Abstract:
Among the Brassica oilseeds, canola (Brassica napus) is the most economically significant globally. However, its production can be limited by blackleg disease, caused by the fungal pathogen Lepstosphaeria maculans. The deployment of resistance genes has been implemented as one of the key strategies to manage the disease. Genetic resistance against blackleg comes in two forms: qualitative resistance, controlled by a single, major resistance gene (R gene), and quantitative resistance (QR), controlled by numerous, small effect loci. R-gene-mediated blackleg resistance has been extensively studied, wherein several genomic regions harbouring R genes against L. maculans have been identified and three of these genes were cloned. These studies advance our understanding of the mechanism of R gene and pathogen avirulence (Avr) gene interaction. Notably, these studies revealed a more complex interaction than originally thought. Advances in genomics help unravel these complexities, providing insights into the genes and genetic factors towards improving blackleg resistance. Here, we aim to discuss the existing R-gene-mediated resistance, make a summary of candidate R genes against the disease, and emphasise the role of players involved in the pathogenicity and resistance. The comprehensive result will allow breeders to improve resistance to L. maculans, thereby increasing yield.
Full text link https://tinyurl.com/45ytx7ap
Article title: DNA-based screening of Brassica germplasm for sustainable and enhanced crop production
Authors: Yueqi Zhang, Ting Xiang Neik, Junrey C Amas, Aldrin Y Cantila, Nur Shuhadah Mohd Saad, Tingting Wu, Jacqueline Batley
Publication title: Plant genetic resources, 2021
Abstract:
The Brassica genus contains many agriculturally important oilseed and vegetable crops. Brassica germplasm, including natural accessions and breeding populations, are maintained globally for sustainable management and enhancement of Brassica crop production, which is critical in meeting the demands of population growth and challenges of environmental stresses due to global climate change. DNA-based markers, such as SNPs, are commonly used to screen large numbers of Brassica germplasm for conservation, genetic mapping and association studies. This chapter focuses on the application of SNP genotyping technologies for conservation of Brassica germplasm, uncovering the genetic basis of various biotic and abiotic stresses and screening for yield-related traits and oil quality through marker-trait association studies.
Full text available upon request to the author/s.
Article title: Genotype main effects and genotype× environment interaction (GGE) analysis for grain yield of the hybrid rice varieties under rain-prone environment
Authors: Aldrin Y. Cantila, Isagane V. Boholano
Publication title: Science & Engineering 14(02):298, 2021
Abstract:
The stability of high yielding hybrid rice varieties is very important to meet food security. The grain yield (GY) stability of 13 hybrid rice varieties in multienvironment with type IV climate condition (E1, E2, E3, and E4) was analyzed using genotype main effects and genotype x environment interaction (GGE). Combined analysis of variance showed environment and genotype by environment (GxE) interaction which accounts 45% and 28% of the total variation, respectively, as the main factors influencing the GY significantly (p< 0.005). GGE biplots were generated using the two interaction principal components (PC1 and PC2) which accounts a total of 92.4% of the GxE effect for GY. GGE biplot analysis identified best performing genotypes for a specific environment like M1 (Mestizo 1), M60 (PAC 801), and M55 (Mestizo 55) at E1 and E2, M60 and M6 (SL-8H) at E3, and M6 at E4. M1 was ranked as top 1, M60 as top 2, M6 as top 3, and M55 as top 4 in four tested environments with a mean GY of 7.48, 7.40, 6.93, and 6.86 t/ha, respectively. Therefore, M1, M60, M6, and M55 should be recommended to rice farm areas of SOCCSKSARGEN and other places in the Philippines with type IV climate condition such as Davao regions.
Full text link https://tinyurl.com/4x92v3ad
Article title: Genetic variation in twenty Philippine traditional rice varieties
Authors: A. Y. Cantila and A. J. R. Quitel
Publication title: Bangladesh Journal of Scientific and Industrial Research 55(1):35-42
Abstract:
The study of genetic variation (GV) in 20 Philippine traditional rice varieties (TRVs) were determined in grain morphology such as length (Gl), width (Gwd), and weight (Gwt), grain yield (Gy), and grain micronutrients such as copper (Cu), iron (Fe), manganese (Mn) and zinc (Zn). Analysis of variance obtained highly significant GV among TRVs in all traits. The mean for Gl, Gwd, Gwt, Gy, Cu, Fe, Mn, and Zn contents was 8.56 mm, 2.8 mm, 20.01 g, 2.13 t/ha, 8.64 ppm, 14.56 ppm, 20.79 ppm, and 30.26 ppm, respectively. The micronutrients in TRVs followed an order as Zn> Mn> Fe> Cu. For the correlation in traits, 11 pairs were significantly correlated; however, only Mn and Zn content in grains was positively and strongly correlated. Other significant pairs were either in positive or negative and moderately correlated. Cluster analysis, on the other hand, revealed five clusters and showed distinct TRV in two clusters. In conclusion, the presence of higher grain micronutrient content in TRVs indicatesa better opportunity for breeders to determine parental genetic resource in breeding rice with high grain micronutrients
Full text link https://tinyurl.com/22vjsm94
Article title: DNA-based screening of Brassica germplasm for sustainable and enhanced crop production
Authors: Yueqi Zhang, Ting Xiang Neik, Junrey C Amas, Aldrin Y Cantila, Nur Shuhadah Mohd Saad, Tingting Wu, Jacqueline Batley
Publication title: Plant genetic resources, 2021
Abstract:
The Brassica genus contains many agriculturally important oilseed and vegetable crops. Brassica germplasm, including natural accessions and breeding populations, are maintained globally for sustainable management and enhancement of Brassica crop production, which is critical in meeting the demands of population growth and challenges of environmental stresses due to global climate change. DNA-based markers, such as SNPs, are commonly used to screen large numbers of Brassica germplasm for conservation, genetic mapping and association studies. This chapter focuses on the application of SNP genotyping technologies for conservation of Brassica germplasm, uncovering the genetic basis of various biotic and abiotic stresses and screening for yield-related traits and oil quality through marker-trait association studies.
Full text available upon request to the author/s.
Article title: Genotype main effects and genotype× environment interaction (GGE) analysis for grain yield of the hybrid rice varieties under rain-prone environment
Authors: Aldrin Y. Cantila, Isagane V. Boholano
Publication title: Science & Engineering 14(02):298, 2021
Abstract:
The stability of high yielding hybrid rice varieties is very important to meet food security. The grain yield (GY) stability of 13 hybrid rice varieties in multienvironment with type IV climate condition (E1, E2, E3, and E4) was analyzed using genotype main effects and genotype x environment interaction (GGE). Combined analysis of variance showed environment and genotype by environment (GxE) interaction which accounts 45% and 28% of the total variation, respectively, as the main factors influencing the GY significantly (p< 0.005). GGE biplots were generated using the two interaction principal components (PC1 and PC2) which accounts a total of 92.4% of the GxE effect for GY. GGE biplot analysis identified best performing genotypes for a specific environment like M1 (Mestizo 1), M60 (PAC 801), and M55 (Mestizo 55) at E1 and E2, M60 and M6 (SL-8H) at E3, and M6 at E4. M1 was ranked as top 1, M60 as top 2, M6 as top 3, and M55 as top 4 in four tested environments with a mean GY of 7.48, 7.40, 6.93, and 6.86 t/ha, respectively. Therefore, M1, M60, M6, and M55 should be recommended to rice farm areas of SOCCSKSARGEN and other places in the Philippines with type IV climate condition such as Davao regions.
Full text link https://tinyurl.com/4x92v3ad
Article title: Phenotypic variation and correlation of traits in Philippine hybrid rice varieties
Authors: Aldrin Y. Cantila, Aizel Mae L. Fordan, Isagane V. Boholano
Publication title: Journal of the Bangladesh Agricultural University 17(2):179-186, 2019
Abstract:
Understanding the phenotypic variation and correlation in hybrid rice varieties will lead to proper utilization of these genetic resources. Grain yield (GY), the primary trait, and its secondary traits such as days to 50% flowering (DF), days to maturity (DM), grain length (GL), grain weight (GW), number of filled grains panicle-1 (NFGP), one thousand grain weight (OTGW) panicle length (PL), panicle weight (PW), spikelet fertility (SF), and spikelet number panicle-1 (SNP) of 13 hybrid rice in two environments (E1 and E2) were analyzed using combined analysis of variance (ANOVA) and correlation analysis. High significant variation was found among hybrids (G) in all traits except for GW while there was at least significant result among environments (E) in DF, DM, GL, GW, PW, and OTGW, and in GxE in DF, DM, GW, NFGP, PW, and SNP. Therefore, E1 hybrids were early flowering and maturing, had longer, wider, and more grains, had longer panicles, and higher yield while in E2 hybrids were late flowering and maturing, and had heavier grains. However, among the 13 hybrid rice, M1 had the highest GY and GL in each environment with a mean of 9.57 t ha–1 and 9.75 mm, respectively. M1, therefore, can be recommended to farmers for varietal utilization. Correlation analysis, on the other hand, found 15 and 17 significant correlations in E1 and E2, respectively. Of the correlation results, it was found out that among the secondary traits, only NFGP was consistently, significantly and positively correlated with GY in two environments. The result implied that attaining higher yield in hybrid rice cultivation can be possible by giving more attention to the plants during the grain filling stage.
Full text link https://tinyurl.com/56xwyc3s
Article title: Assessing genetic diversity of asian-based rubber populations using SSR and multivariate statistics in the Philippines
Authors: Aldrin Y. Cantila, Rene Rafael C. Espino, Emma K. Sales
Publication title: Journal of Biology, Agriculture and Healthcare, 6:16, 2016
Abstract:
Assessing genetic diversity of rubber populations is important for the effective utilization of rubber genetic resources. Diversity indices such as number of alleles (Na), observed heterozygosity (Ho), gene diversity (GD), polymorphism information content (PIC) and power of discrimination (PD) along with multivariate statistics such as principal component analysis (PCA) and clustering analysis were used in the study. Twenty-two SSR markers had means 5.09 Na, 0.579 Ho, 0.677 GD, 0.643 PIC and 0.785 PD for 63 rubber clones comprised of 34 Indonesian and 29 Malaysian clones. Malaysian subpopulation had 3.59 Na per clone greater than Indonesian subpopulation of 2.97 Na per clone. PCA detected 66.08% total variation for eight principal components (PCs). PC1, PC2 and PC3 contributed 13.24% variation (v) with 2.91 eigenvalue (e), 10.2% v with 2.24 e and 8.86% v with 1.95 e, respectively. Clustering analysis revealed 0.237 genetic similarity and ten clusters for all clones. Clusters will be the basis for making more genetically diverse hybrids while PC1 member clones will be the basis for considering genetically broad base parent. The high genetic diversity found in the Asian-based rubber populations and complementing results of multivariate statistics can optimize the selection and breeding of rubber genetic resources in the Philippines.
Full text link https://tinyurl.com/5n6u4zet
Article title: Multiple Statistical Tools for Divergence Analysis of Rice (Oryza sativa L.) Released Varieties
Authors: Aldrin Y. Cantila, Sailila E. Abdula, Haziel Jane C. Candalia and Gina D. Balleras
Publication title: The Philippine Statistician 65(2):121-134, 2016
Abstract:
Rice released varieties are genetic resources bulked with good genes. To define the potentials of these germplasm, genetic divergence analysis must be done. The study used different statistical tools such as descriptive statistics, Kolmogorov-Smirnov test, Shannon-Weaver diversity index (H’), correlation statistics (r), principal component analysis (PCA), Dixon’s test and clustering statistics in evaluating 29 NSIC (National Seed Industry Council) released varieties based on 11 morphological traits. Descriptive statistics showed significant differences on the traits used while following a normal distribution. Shannon-Weaver diversity derived a range of 0.55 (number of filled grain per panicle, NFGP) to 0.91 (grain yield, GY and number of tillers, NT) that infer moderate to high diversity traits. Correlation statistics among traits showed a range of r = -0.55 to 0.84 which GY was noted to positively correlate to all traits. PCA accounted 39.95% and 26.10% for PC1 and PC2, respectively. Notable component loading for the yield component traits such as panicle weight (PW) showed the highest contributor of positive projections in two PCs that explained 66.05% of the variation. PCA also detected two latent traits such GY and spikelet fertility (SF) as confirmed in Dixon’s test where outlier was found in SF and to yield contributing traits. Clustering statistics separated varieties into 5 clusters with a range of 5.88 to 106.22 euclidean distance (ED). Among the clusters, 5th cluster composed of one variety, NSIC Rc240 gave the highest GY (7.07 tha-1), NFGP (152.67), one thousand grain weight (24.77 g), PW (5.08 g) and spikelet number per panicle (185.33). The variety could potentially be adapted and a good source of genes for rice improvement localize at General Santos City.
Full text link https://tinyurl.com/2fkdsjmx
Article title: Statistical Analysis of Foreign Rice Phenotypes under Different Seasons of the Philippines
Authors: Aldrin Cantila, Alvin John R. Quitel
Publication title: Journal of Advanced Applied Scientific Research 1(12), 2017
Abstract:
Korean rice is a foreign genetic resources in the Philippines that has to be characterized for its proper germplasm utility. Ten Korean phenotypes were analyzed using correlation, clustering and principal component analyses (PCA) based on the 13 traits viz., culm length (CL), days to 50% flowering (D50F), days to maturity (DM), filled grains per panicle (FGP), flag leaf length (FLL), flag leaf width (FLW), grain length (GL), grain width (GW), grain yield (GY), plant height (PH), productive tillers (PT), spikelet fertility SF) and thousand grain weight (TGW) under different seasons of the Philippines. It was found out that Korean phenotypes had earlier D50F and DM, shorter PH and CL, more PT, FGP and SF, and higher GY under dry than wet season. Each season had three groups based on the clustering analysis with a pattern of group 1 having phenotypes with heavy TGW, early D50F and DM, short PH and FLL; and more FGP, SF and GY; group 2 having long CL, wide FLW, light TGW; and late D50F and DM; and group 3 having short CL, narrow FLW and low PT. Correlation in FGP, PT and SF to GY was consistently high positive (r≥ 0.68) in two seasons. Also, PCA consistently showed that GY, PH and PT were the highest contributor of variation with an average of 21.42% in two seasons. Korean GY therefore was highly variable but attaining higher GY can be possible by utilizing grain-filling (FGP and SF) and productive tillering (PT) traits as selection indices in the breeding program.
Full text link https://tinyurl.com/mu54a3s5
Article title: Morphometric analysis of upland rice phenotypes in lowland condition
Authors: Aldrin Y. Cantila, Sailila E. Abdula, Jenalyn L. Balos
Publication title: Journal of Biodiversity and Environmental Sciences 10(4):62-69, 2017
Abstract:
Knowledge about upland characters expressed in an unfavorable environment will direct to appropriate utilization of upland rice varieties (URVs) for breeding and improvement. Morphometric analysis of 55 URVs in lowland condition was done using different statistical parameters such as basic statistics (standard deviation, coefficient of variation and ANOVA), Shannon-Weaver diversity coefficient (H’), principal component analysis (PCA) and clustering analysis based on 14 characters. H’ values were ranged from 0.69 (flag leaf width, FLW) to 0.95 (grain yield, GY), indicating a medium to high diversity characters. PCA captured 84.78% variation for six principal components (PC), retained using proportion of variance and eigenvalues >1.0.Grain length (GL), grain width (GW) and grain size ratio (GSR) formed PC1 and days to 50% flowering (DF), days to maturity (DM) and thousand grain weight (TGW)formed PC2. PCA found that grain attributes (GL, GW, GSR and TGW) followed by DF and DM were highly affected. Clustering analysis grouped varieties into four. The results therefore could be used especially on deciding what URV is to be utilized for any rice breeding program in lowland conditions.
Full text available upon request to the author/s.
Article title: The Study of Quantitative Traits with Different Statistical Parameters in Registered Inbred Rice (Oryza sativa L.)
Authors: Aldrin Y. Cantila, Sailila E. Abdula, and Haziel Jane C. Candalia
Publication title: Philippine Journal of Science 146(4):387-393, December 2017
Abstract:
The primary quantitative trait grain yield (GY) and secondary traits viz., days to maturity (DM),
number of productive tillers (NPT), plant height (PH), panicle weight (PW), spikelet fertility (SF),
spikelet number per panicle (SNP), and thousand seed weight (TSW) of 18 Philippine registered
inbred rice were studied using different statistical parameters viz., correlation analysis, genotypic and phenotypic coefficient of variability (GCV and PCV), broad sense heritability (H2b), and genetic advance (GA). There was a significant, positive, and strong correlation between DM and PH, PW and SNP, PW and GY, and SNP and GY. GCV showed moderate variability in PW with 11.94% and NPT with 10.55%. PCV also showed moderate variability in NPT with 17.23%, GY with 14.3%, PW with 13.89% and SNP with 12.67%. All traits except for PW and SNP in GCV and traits except for NPT, GY, PW, and SNP in PCV showed low variability. H2b too had PH with 79.26%, PW with 73.91%, and SNP with 60.39% as high heritability while GA expressed to the mean (GAM) had PW with 21.14% as high genetic gain. The study found out that PW and SNP had positive and strong association to GY, but only PW had consistent and considerable amount of genotypic and phenotypic variations. Furthermore, high H2b along with high GAM was only obtained in PW. Therefore, the different statistical parameters were in congruent with the implication that higher grain yield can be achieved by attaining genotypic selection in PW
Full text link https://tinyurl.com/4ttb8ty8
Article title: Transgressive segregants: a potential approach in yield mining
Authors: Abdula, S.E., Balos, J.L., Cantila, A.Y., Ramos, M.R.; et al.
Publication title: Philippine Journal of Crop Science 42(supplement 1), 2017
Abstract:
Transgressive segregation is the formation of extreme or transgressive phenotypes, observed in segregated hybrid populations compared to phenotypes observed in the parental lines (Nolte et al; 2005 and Rieseberg et al; 1999). This phenomenon is specific to segregating hybrid generations and refers to that fraction of individuals that exceed parental phenotypes values in either a negative or positive fashion (Doyle and Gaut, 2000). Using ten FI hybrid rice varieties, this research aimed to identify and select possible transgressive segregants after several planting of segregating population with yield and phenotype equal to or better than the original FI hybrids. After F6 generation of planting and selection, a total of 366 candidate transgressive lines were selected and evaluated for general yield trial in six different sites. Twenty-two high yielding transgressive lines were identified with yield advantages ranging from 10-30%. Further, AMMI analysis of variance for grain yield tested in these environments showed that mean effects of G and R accounted for 0.96% and 79.19% variations, respectively and GXE interaction effects represent 1.88% of the total variation. Furthermore, the variance due to environments were diverse into large differences on the mean yield between environments causing most of the variation in the grain yield, indicating that there were viable differences in the genotype response across environments. Moreover, the presence of GEI was clearly demonstrated by the AMMI model, when the interaction was partitioned among the five interaction principal component axis (IPCA).
Full text available upon request to the author/s.
Article title: Molecular Evaluation of the Philippine Best Rubber Clones using Genomic-based Simple Sequence Repeats
Authors: Aldrin Yanong Cantila, Rene C. Espino, Emma K. Sales
Publication title: Journal of Advanced Applied Scientific Research 1(11):9-27, 2017
Abstract:
University of Southern Mindanao Agricultural Research Center, Philippines conserved 86 rubber clones in the field germplasm. Among rubber clones, only seven were commercially released and widely utilized by Filipino rubber farmers. Nineteen genomic-based simple sequence repeats (G-SSRs) provided enough data onto evaluating molecular information of Philippine best rubber clones (five PB, one RRIM and one Philippine or Phil derived clones) along with two RRIM and Phil check clones. G-SSRs derived 72 alleles in all with means N, Ne, Ho, and PIC of 3.789, 2.284, 0.569 and 0.508 per G-SSR, respectively. Nine G-SSRs however detected 16 private alleles across rubber clones and groups that led AMOVA result to 74.37% molecular variance within clones. Private alleles in best clones could be used as molecular reference to authenticate registered clones especially in nursery farm-producing planting materials. Genetic relationship was in a range of 0.184 to 0.487 proximities, having PB217 and SMRX1 as the closest. Bayesian structure analysis on the other hand distributed clones into two groups (group 1- RRIM600, RRIM712 and RRIM901; group 2- PB217, PB235, PB260, PB311, PB330, SMRX1, UPLBPlant1 and USM1); a reference for in-depth consideration of making crosses.
Full text link https://tinyurl.com/23ucvc37
Article title: Assessing genetic diversity of asian-based rubber populations using SSR and multivariate statistics in the Philippines
Authors: Aldrin Y. Cantila, Rene Rafael C. Espino, Emma K. Sales
Publication title: Journal of Biology, Agriculture and Healthcare, 6:16, 2016
Abstract:
Assessing genetic diversity of rubber populations is important for the effective utilization of rubber genetic resources. Diversity indices such as number of alleles (Na), observed heterozygosity (Ho), gene diversity (GD), polymorphism information content (PIC) and power of discrimination (PD) along with multivariate statistics such as principal component analysis (PCA) and clustering analysis were used in the study. Twenty-two SSR markers had means 5.09 Na, 0.579 Ho, 0.677 GD, 0.643 PIC and 0.785 PD for 63 rubber clones comprised of 34 Indonesian and 29 Malaysian clones. Malaysian subpopulation had 3.59 Na per clone greater than Indonesian subpopulation of 2.97 Na per clone. PCA detected 66.08% total variation for eight principal components (PCs). PC1, PC2 and PC3 contributed 13.24% variation (v) with 2.91 eigenvalue (e), 10.2% v with 2.24 e and 8.86% v with 1.95 e, respectively. Clustering analysis revealed 0.237 genetic similarity and ten clusters for all clones. Clusters will be the basis for making more genetically diverse hybrids while PC1 member clones will be the basis for considering genetically broad base parent. The high genetic diversity found in the Asian-based rubber populations and complementing results of multivariate statistics can optimize the selection and breeding of rubber genetic resources in the Philippines.
Full text link https://tinyurl.com/5n6u4zet
Article title: Multiple Statistical Tools for Divergence Analysis of Rice (Oryza sativa L.) Released Varieties
Authors: Aldrin Y. Cantila, Sailila E. Abdula, Haziel Jane C. Candalia and Gina D. Balleras
Publication title: The Philippine Statistician 65(2):121-134, 2016
Abstract:
Rice released varieties are genetic resources bulked with good genes. To define the potentials of these germplasm, genetic divergence analysis must be done. The study used different statistical tools such as descriptive statistics, Kolmogorov-Smirnov test, Shannon-Weaver diversity index (H’), correlation statistics (r), principal component analysis (PCA), Dixon’s test and clustering statistics in evaluating 29 NSIC (National Seed Industry Council) released varieties based on 11 morphological traits. Descriptive statistics showed significant differences on the traits used while following a normal distribution. Shannon-Weaver diversity derived a range of 0.55 (number of filled grain per panicle, NFGP) to 0.91 (grain yield, GY and number of tillers, NT) that infer moderate to high diversity traits. Correlation statistics among traits showed a range of r = -0.55 to 0.84 which GY was noted to positively correlate to all traits. PCA accounted 39.95% and 26.10% for PC1 and PC2, respectively. Notable component loading for the yield component traits such as panicle weight (PW) showed the highest contributor of positive projections in two PCs that explained 66.05% of the variation. PCA also detected two latent traits such GY and spikelet fertility (SF) as confirmed in Dixon’s test where outlier was found in SF and to yield contributing traits. Clustering statistics separated varieties into 5 clusters with a range of 5.88 to 106.22 euclidean distance (ED). Among the clusters, 5th cluster composed of one variety, NSIC Rc240 gave the highest GY (7.07 tha-1), NFGP (152.67), one thousand grain weight (24.77 g), PW (5.08 g) and spikelet number per panicle (185.33). The variety could potentially be adapted and a good source of genes for rice improvement localize at General Santos City.
Full text link https://tinyurl.com/2fkdsjmx