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% influenced by GL, 37.4% influenced by GW, and 49.1% influenced by GT. Hence, assuming the trend of trait selection, i.e., GT > GW > GL, for improving TGW in the rice yield enhancement programs. The InDel markers successfully identified a total of 38 alleles, out of which 27 alleles were major and were found in more than 20 genotypes. GL was associated with four genes (GS3, GS7, GW8, and GS2). GT was also found to be regulated by four different genes (GS3, GS7, GW8, and GS2) out of the nine studied genes. GW was found to be under the control of three studied genes (GW5, GW8, and GS2), whereas TGW was found to be under the influence of four genes (SLG7, GW5, GW8, and GS5) in the germplasm under study. The Unweighted Pair Group Method with Arithmetic means (UPGMA) tree based on the studied InDel marker loci segregated the whole germplasm into three distinct clusters with dissimilar grain sizes and weights. A two-dimensional scatter plot constructed using Principal Coordinate Analysis (PCoA) based on InDel markers further separated the 204 rice germplasms into four sub-populations with prominent demarcations of extra-long, long, medium, and short grain type germplasms that can be utilized in breeding programs accordingly. The present study could help rice breeders to select a suitable InDel marker and in formulation of breeding strategies for improving grain appearance, as well as weight, to develop rice varieties to compete international market demands with higher yield returns. This study also confirms the efficient application of InDel markers in studying diverse types of rice germplasm, allelic frequencies, multiple-gene allele contributions, marker-trait associations, and genetic variations that can be explored further.

Genotype × Environment (G×E) interaction and stability performance were investigated on paddy yield of eighteen rice genotypes and twelve locations using two well renowned statistical models; genotype main effect and G×E Biplot analysis (GGE) and additive main effects and multiplicative interaction (AMMI) analysis. The aim of this study was to elucidate the performance of some advance rice lines/genotypes at multiple locations in multi environment trials (METs) using GGE biplot and AMMI analyses. The results of GGE biplot and AMMI analyses performed over the data of paddy yield at multiple locations of two years 2014 and 2015 indicated that G×E interaction plays a crucial role in determining the performance of genetic material in METs. The results declare that GGE and AMMI not only provide easy and affective evaluation of genotypes into environment interactions in a number of locations but also a comprehensive understanding of the variability of the target locations. AMMI analyses for data of both years indicated that RRI 7 was the highest priority selected genotype for six locations, NIAB 1175 for four and RRI 3 for three locations. Dhokri and Kala Shah Kaku were the highest yielding, while Faisalabad and Dhokri were the most stable environments in 2014. Likewise, Faisalabad and PARC Islamabad were the highest yielding as well as most stable environments in 2015. Basmati 515 and PS 2 were the most favorable genotypes in 2014 and 2015, respectively for their high paddy yield and stability at all locations. The results further suggested that both models were useful and presented similar interpretations about MET data. Key words: Genotype main effect and G × E biplot analysis (GGE), additive main effects and multiplicative interaction (AMMI) analysis, rice, fine type, multiple locations.

Regarding rice grown in five different locations, rice quality is measured using an auto grain analyzer. Auto grain analyzer works on the Near-Infrared transmittance (720 -1100 nm). Protein, amylose and moisture contents of the rice samples of nine (9) fine lines were tested. Different environment tested entries were evaluated and found that all the values have highly significant effect of environment and genotypes. The environment and genotype ranking in the Additive Main effect and Multiplicative Interaction (AMMI) model were studied and PK8680-13-3-1 and check variety Basmati 515 were found to be most stable lines in most micro environment with respect to amylose contents and moisture contents. Protein contents were studied in PK8892-4-2-1-1 and PK3810-30-1 and are best suited in all the environments. The results indicated that grain analyzer may be used for amylose and protein contents along with effect of different locations on these traits in early breeding generations for quality control in the food industry.

In the present study, genetic parameters, agro-morphologic stability and clustering pattern of twenty promising elite basmati rice (Oryza sativa L.) lines including three checks were investigated in advance generation. Triplicated randomized complete block design (RCBD) was used during three consecutive years from 2016 to 2018 and the data were subjected to combined ANOVA, correlation, principal component, GGE biplots in order to demonstrate the stability and performance of these advance Basmati lines. A highly significant and exploitable level of genetic variability was found existed among tested inbred lines. Higher broad sense heritability (%) was observed among tested genotypes which specifies higher proportion of phenotypic variation attributed by genetic values. Correlation matrix portrayed significantly positive relationship of grain yield with maturity days; significantly positive relationship of plant height with days to maturity and highly negative with panicle length and thousand grains weight. Dendrograms divided the genotypes into six distinct Clusters. Based on GGE biplots, PK10324-1-1 followed by PK9444-8-1-2 and PK10029-13-2-1 were identified to be most superior and potential candidate Basmati lines with better yield and stability across three years (growing seasons). Whereas, Super Basmati (check), PK 10436-2-1-1, PK10437-14-2-1 exhibited lowest yield stability across test environments. Test-environment analysis indicated that genotypes PK10324-1-1 and PK9444-8-1-2 were best suited for 2017 season, genotypes PK10967-30-1, Chenab Basmati and PK 10355-13-2-1 were best suited for 2018, genotypes PK9966-10-1 and PK 10434-6-2-1 were best suited for 2016 season, whereas genotype PK10029-13-2-1 performed equally well in 2017 and 2018. Principal Component Analysis (PCA) also displayed stability in performance relative to all studied traits in all the advance Basmati lines. Convincingly, the higher yielding and more stable among the studied advance Basmati lines can be utilized as new candidate Basmati lines as compared to existing Basmati verities used as checks.

Rice is food for more than half of the world population and the most consumable cereal in most of the countries. Pakistan is the fifth largest exporter of rice. However, Bacterial leaf blight (BLB) caused by Xanthomonas oryzae pv. oryzae is the most devastating and serious threat to rice production in many countries of the world including Pakistan. To combat this disease, innate genetic resistance of the plant plays vital role along with being environmentally friendly and economical. In this study, thirty-one (31) Near Isogenic Lines (NILs) having Xa4, xa5, Xa7, xa13 and Xa21 reported BLB tolerant genes and 34 locally developed rice lines were investigated under natural field conditions at three agro-ecologically different locations with highest disease occurrence records (BLB hotspots) viz., Sheikhupura, Hafizabad and Gujranwala, Punjab, Pakistan in order to assess their respective genetic resistance and G × E interactions against the disease. Thirty-one (31) lines were categorized under resistant cluster, twenty-eight (28) were moderately resistant, six (6) were moderately susceptible and one (susceptible check) was in susceptible category. Grouping of different lines/varieties under same cluster shows their significantly similar response against BLB disease in corresponding environment. Among the studied NILs, only one line showed polymorphism for all five resistant genes, two lines had four; seven lines had three genes, seven lines showed di-genic while five lines showed mono-genic polymorphism. These resistant lines with multiple-genes for BLB resistance can be evolved as a new BLB resistant variety and also be utilized as donor parent in breeding programs for developing new cultivars with horizontal resistance against more than one target pathotypes and environments.