Grain appearance is one of the most important attributes of rice. It is determined by grain size,... more Grain appearance is one of the most important attributes of rice. It is determined by grain size, shape, and weight, which in turn influences the rice yield and market value. In this study, QTLs for grain length, grain width, grain length/width ratio, and grain weight were mapped using the high-throughput indica/indica SNP platforms. The population of the mega indica variety IR64 and the high-quality aromatic variety Sadri from Iran was phenotyped. Based on this phenotypic data, plants of 94 F2:3 families including both parents were selected. A linkage map analysis of 210 SNP markers identified 14 QTLs controlling the grain length, grain width, length/width ratio, and 1,000 grain weight. Among these 14, one important region containing the QTLs for all the four studies’ traits was mapped on chromosome 8. It was derived from Sadri for the decreased length/width ratio and increased grain weight. This study demonstrated the speed and efficiency in using multiplex SNP genotyping for QTL ...
In light of the rapidly growing global population, there is an urgent need to develop high-yieldi... more In light of the rapidly growing global population, there is an urgent need to develop high-yielding and climateresilient rice varieties. The productivity of traditional basmati cultivars is limiting due to region-specific cultivation, and genetic improvements are direly needed to enhance their productivity without compromising quality attributes. This study aimed to develop high yielding basmati advance line with good quality attributes through a marker-assisted selection approach. A cross was attempted between Basmati 515 and IRBB 66, followed by pedigree selection up to the F5 generation. A uniform recombinant inbred line was identified then backcrossed with PK 1121 Aromatic and again followed by pedigree selection up to BC3F5 for desirable genotype development. Genes pyramiding for aroma (BADEX7-5), dense and erect panicles (DEP1), grain length (FMGS7) and grain width (GW8-indel) were achieved using gene-linked markers. The identified line “BLB 18-5001”, predominately harbored ag...
Authors' Contribution MR, BA and AMS conceptualized the study. MR and BA recorded the data. AMS a... more Authors' Contribution MR, BA and AMS conceptualized the study. MR and BA recorded the data. AMS and MS statistical analyzed the data. MR, MT and MYA wrote introduction section of the manuscript. MR, BA and MT wrote methodology section of the manuscript. MR, BA, AMS and MA wrote results and discussion section of the manuscript.
Drought is one of the major abiotic threat to rice production in the context of climate change. S... more Drought is one of the major abiotic threat to rice production in the context of climate change. Super Basmati is an elite, fine grain basmati rice variety grown in Punjab, Pakistan. Due to drought sensitive in nature, its yield has been facing an alarming situation in production because of gradual decrease in irrigated water for a couple of years. Three reported novel QTLs for drought tolerance were selected for incorporation into Super Basmati by employing marker assisted selection strategy. IR55419-04 with novel QTLs was used as a donor parent. Foreground selection was performed by applying PCR based QTL linked SSR markers followed by recombinant selection by using 2-4 flanking markers. Background selection was exercised by using polymorphic SSR markers for maximum genome recovery of the Super Basmati. The individuals homozygous at the target QTLs and with maximum background of Super Basmati at the rest of the non-target genome was selected for evaluation of drought tolerance. Under drought stress conditions, the yields of all introgressed lines (ILs) were 44.2%-125.7% higher than recurrent parent. Six superior ILs that are drought tolerant and very similar to Super Basmati in terms of agronomic and grain quality traits are marked for release as drought-tolerant varieties in arid regions or for use in breeding programs of high grain quality and drought-tolerant parents.
R ice (Oryza sativa L.) is a staple food crop of more than half of the inhabitants across the glo... more R ice (Oryza sativa L.) is a staple food crop of more than half of the inhabitants across the globe (Khush, 2004). In Pakistan, after wheat, it occupies 2 nd position. Its cropped area was 3034 M ha and production was 7.410 M tons (Economic Survey of Pakistan, 2019). Among the cereal crops, rice is an important export commodity (Economic Survey of Pakistan, 2019). It contributes 3.1% in value addition to agriculture and 0.6% in the GDP (Economic Survey of Pakistan, 2019). The average yield of rice in Pakistan is about 2.44 t ha -1 (Economic Survey of Pakistan, 2019) which is low as compared to other rice producing countries due to many constraints including proper crop establishing techniques . In Asia rice is growing by transplanting, rice seedlings manually in puddled soil which is a widely adopted method. It consumes abundant water . Whereas, water resources are declining day by day. Its judicious use is gaining a pivotal importance to fulfil future water and food demand for the growing population . Shrinking water resources availability is a threat for the future rice production in Asia and will adversely affect the sustainability of Abstract | Planting method is an important aspect of production technology for the maximum resource utilization by crops per unit area. Dry-seeded rice (DSR) is a contemporary resource saving crop establishing technique, which enables farmers to harvest economical rice production. Field study was conducted at Rice Research Institute, Kala Shah Kaku, Pakistan in 2014 and in 2015 to evaluate the different planting methods. Three dry-seeded rice (DSR) planting methods viz. (i) DSR-broadcast, (ii) DSR-drill, (iii) DSR-ridges were compared with the conventional transplanting (TR) method in lines having row to row and plant to plant distance of 22.5cm distance, and farmer transplanting method. Experimental design was randomized complete block, replicated 3 times. Data were recorded on height (cm), tillers m -2 , filled and unfilled grains panicle -1 , thousand grain weight (g), grain and biomass yield (t ha -1 ). Grain sterility (%) and harvest index (%) were also calculated. Highest grain yield (5.00 to 5.11 t ha -1 ) with harvest index (30.00 to 31.50%) and relatively low grain sterility (12.00 to 12.01%) were observed in DSR-ridge and DSR-drill sowing method. Moreover, DSR (i.e. DSR-ridge and -drill) resulted in 104 and 76 % more profit over TR-farmer practice. The study concluded that DSR-ridge and DSR-drill proved to be the best to obtain the maximum paddy yield and net profit. Farmers can adopt these methods to harvest maximum benefit.
Sogatella furcifera Horvath and brown planthopper (BPH) Nilaparvata lugens Stål. Rice planthopper... more Sogatella furcifera Horvath and brown planthopper (BPH) Nilaparvata lugens Stål. Rice planthoppers are considered as severe and notorious insect pests of rice crop (Sabir et al., 2016). These planthoppers have also achieved the status of most destructive pests in rice crop (
Rice holds the key to future food security. In rice-growing areas, temperature has already reache... more Rice holds the key to future food security. In rice-growing areas, temperature has already reached an optimum level for growth, hence, any further increase due to global climate change could significantly reduce rice yield. Several mapping studies have identified a plethora of reproductive tissue-specific and heat stress associated inconsistent quantitative trait loci (QTL), which could be exploited for improvement of heat tolerance. In this study, we performed a meta-analysis on previously reported QTLs and identified 35 most consistent meta-QTLs (MQTLs) across diverse genetic backgrounds and environments. Genetic and physical intervals of nearly 66% MQTLs were narrower than 5 cM and 2 Mb respectively, indicating hotspot genomic regions for heat tolerance. Comparative analyses of MQTLs underlying genes with microarray and RNA-seq based transcriptomic data sets revealed a core set of 45 heat-responsive genes, among which 24 were reproductive tissue-specific and have not been studied...
Rice is critical for sustainable food and nutritional security; however, nominal micronutrient qu... more Rice is critical for sustainable food and nutritional security; however, nominal micronutrient quantities in grains aggravate malnutrition in rice-eating poor populations. Here, we assessed genetic diversity in grain iron (Fe) and zinc (Zn) contents using trait-linked simple sequence repeat (SSR) markers in 56 fine and coarse grain rice accessions of different geographical origin. Aromatic fine gain accessions contained relatively higher Fe and Zn contents in brown rice (BR) than coarse grain accessions. Genotyping with 24 SSR markers identified 21 polymorphic markers, among which seventeen demonstrated higher gene diversity and polymorphism information content (PIC) values, strongly indicating that markers used in current research were moderate to highly informative for evaluating genetic diversity. Population structure, principal coordinate and phylogenetic analyses classified studied rice accessions into two fine grain specific and one fine and coarse grain admixture subpopulatio...
Basmati rice is treated as one of the world’s best rice due to its extra-long grain and unique ar... more Basmati rice is treated as one of the world’s best rice due to its extra-long grain and unique aroma,. Over the last decade, Pakistan has earned more than US$2 billion through basmati export. Unfortunately, basmati rice is being threatened with bacterial leaf blight (BLB) disease that leads to poor production and quality. We attempted pyramiding of BLB genes through marker-assisted backcross breeding using Super Basmati as the recipient and IRBB60 as the donor parent. BLB resistance genes Xa4, xa5, and Xa21 were used for introgression. Molecular markers MP1 and MP2, RM122, and pTA248 were used for Xa4, xa5, and Xa21 genes respectively for foreground selection. The 85 SSR polymorphic molecular markers were used for background selection, which showed a more than 90% recurrent parent genome recovery. Phenotypic traits for grain dimensions were also considered while selecting backcross female parents from BC1F1 to BC5F1, which resulted in saving the resources from background selection before the selfing of backcrossed lines. Multiple lines carrying BLB resistance genes combinations Xa4 + xa5 and Xa4 + xa5 + Xa21 were developed. The BC5F4 uniform lines showed resistance against BLB disease at hotspot locations. One of the developed lines, PKBB15–116, which has a yield advantage of more than 10%, tolerant to lodging, and has basmati quality. These pyramided lines in basmati background will also be helpful for breeders to incorporate resistance genes in a shorter period of time, in order to develop new basmati rice varieties in future.
Biofortification of staple crops with essential micronutrients is the sustainable way to overcome... more Biofortification of staple crops with essential micronutrients is the sustainable way to overcome the hidden hunger. A large number of quantitative trait loci (QTL) linked with grain micronutrient contents have been reported in different mapping studies. Identification of consistent QTLs across diverse genetic backgrounds is useful for candidate gene analysis and marker assisted selection of target traits. In this study, an up to date meta-analysis of grain iron and zinc associated QTLs was performed and 48 meta-QTLs (MQTLs) distributed across 12 rice chromosomes were identified. The 95% confidence intervals of identified genomic regions were significantly narrower than the average of their corresponding original QTLs. A total of 9308 genes/transcripts physically located within or near MQTL regions were retrieved and through prioritization of candidate genes (CGs) 663 non-redundant iron and zinc CGs were selected and studied in detailed. Several functionally characterized iron and zinc homoeostasis related genes e.g OsATM3, OsDMAS1, OsFRO2, OsNAS1-3, OsVIT2, OsYSL16, OsZIP3 and OsZIP7 were also included in our MQTL analysis. More than 64% genes were enriched with zinc and iron binding gene ontology terms and were involved in oxidation reduction process, carbohydrate metabolic process, regulation of transcription, trans-membrane transport, response to oxidative stress, cell redox homeostasis and proteolysis etc. In-silico transcriptomic analysis of rice identified 260 CGs which were regulated in response to iron and zinc stresses. We also identified at least 37 genes which were differentially expressed under both stress conditions and majority of these have not been studied in detailed before. Our results strongly indicate that majority of the MQTLs identified in this study are hotspots for grain iron and zinc concentration and are worth of intensive functional studies in near future.
Rice is food for more than half of the world population and the most consumable cereal in most of... more 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.
Journal of Experimental Biology and Agricultural Sciences, 2019
Rice is the staple food for half of the world"s population, however, its edible grain part is def... more Rice is the staple food for half of the world"s population, however, its edible grain part is deficient in essential micronutrients, especially Fe and Zn. Breeding for micronutrient dense rice demands exploration of available genetic diversity for grain Fe, Zn and β-carotene contents. In this study, we analysed brown and polished grain samples of 26 traditional rice genotypes for Fe and Zn concentration. Fe concentration varied from 13.23 ppm to 45.83 ppm and 1.10 ppm to 36.45 ppm in brown and polished rice, respectively. Whereas, Zn concentration in brown and polished rice ranged from 18.67 ppm to 38.01 ppm and 5.86 ppm to 23.88 ppm, respectively. The landraces had higher Fe and Zn contents than improved varieties and advance uniform lines. Significant positive correlation was present between Fe and Zn concentration in brown (r = 0.694, P < 0.01) and polished rice (r = 0.533, P < 0.01). Fe concentration was greatly reduced by the polishing process than Zn concentration and approved varieties lost less Fe and Zn contents than advance uniform lines. Minimal levels of beta-carotene were detected in rice genotypes indicating need for genetic modifications to enhance pro-vitamin A contents in rice endosperm.
Xanthomonas oryzae pv. oryzae (Xoo) has now become one of major rice diseases. During recent year... more Xanthomonas oryzae pv. oryzae (Xoo) has now become one of major rice diseases. During recent years, its occurrence has increased in Pakistan, particularly in 'Kallar tract' which is well-known for quality rice cultivation. Development of new resistant varieties by utilizing the available resistant gene-pool is most reliable breeding technique for the plant breeders. The present study was conducted to explore the genetic resources regarding presence and absence of BLB resistance genes Xa4, xa5 and Xa21 through DNA marker technology. Effectiveness of Xa21 followed by xa5 and Xa7 genes has been reported to confer more resistance level for BLB in traditional rice belt of Pakistan. For this purpose, eighty (80) rice genotypes comprising of diverse origin including three isogenic lines viz., IRBB4 (carrying Xa4), IRBB5 (carrying xa5) and IRBB21 (carrying Xa21) as positive resistant gene checks and IR24 (carrying none of these) as negative gene check were genotyped. DNA fingerprinting results indicated the presence of Xa4 gene in 41 entries, while 14 lines were positive for xa5 gene. Only one local line was carrying Xa21 gene along with Xa4. Thus, the present study will not only be helpful for rice breeders to develop new rice varieties carrying disease resistant genes, but will also provide the donors to incorporate / pyramid disease resistant genes in popular rice varieties like Super Basmati and Basmati 515 which are susceptible to BLB disease.
Chemical mutagens have long been used to create genetic variability in crop plants for breeding r... more Chemical mutagens have long been used to create genetic variability in crop plants for breeding research and genetic studies. In rice, more than 500 varieties have been released through induced mutations. Ethyl methane sulphonate (EMS) is the most commonly used chemical mutagen in plants. EMS normally induces Gas chromatography GC to AT transitions in the genome and thus resulting protein in the mutant plant has different functions than normal. The present study was carried out to investigate the mutagenic effects of different concentrations of EMS on germination and yield parameters of two basmati rice cultivars (Super basmati and Basmati 370). The seeds were subjected to different treatment levels of EMS. The treated and untreated plants were observed under different agronomic parameters. EMS was quite effective in inducing genetic variability in Basmati rice. The results revealed significant difference among all the traits studied. The efficiency of EMS was found to depend upon its concentration and it was higher at lower concentration in both genotypes. The study further revealed that the use of EMS is an effective approach for creating new rice germplasm.
Grain appearance is one of the most important attributes of rice. It is determined by grain size,... more Grain appearance is one of the most important attributes of rice. It is determined by grain size, shape, and weight, which in turn influences the rice yield and market value. In this study, QTLs for grain length, grain width, grain length/width ratio, and grain weight were mapped using the high-throughput indica/indica SNP platforms. The population of the mega indica variety IR64 and the high-quality aromatic variety Sadri from Iran was phenotyped. Based on this phenotypic data, plants of 94 F2:3 families including both parents were selected. A linkage map analysis of 210 SNP markers identified 14 QTLs controlling the grain length, grain width, length/width ratio, and 1,000 grain weight. Among these 14, one important region containing the QTLs for all the four studies’ traits was mapped on chromosome 8. It was derived from Sadri for the decreased length/width ratio and increased grain weight. This study demonstrated the speed and efficiency in using multiplex SNP genotyping for QTL ...
In light of the rapidly growing global population, there is an urgent need to develop high-yieldi... more In light of the rapidly growing global population, there is an urgent need to develop high-yielding and climateresilient rice varieties. The productivity of traditional basmati cultivars is limiting due to region-specific cultivation, and genetic improvements are direly needed to enhance their productivity without compromising quality attributes. This study aimed to develop high yielding basmati advance line with good quality attributes through a marker-assisted selection approach. A cross was attempted between Basmati 515 and IRBB 66, followed by pedigree selection up to the F5 generation. A uniform recombinant inbred line was identified then backcrossed with PK 1121 Aromatic and again followed by pedigree selection up to BC3F5 for desirable genotype development. Genes pyramiding for aroma (BADEX7-5), dense and erect panicles (DEP1), grain length (FMGS7) and grain width (GW8-indel) were achieved using gene-linked markers. The identified line “BLB 18-5001”, predominately harbored ag...
Authors' Contribution MR, BA and AMS conceptualized the study. MR and BA recorded the data. AMS a... more Authors' Contribution MR, BA and AMS conceptualized the study. MR and BA recorded the data. AMS and MS statistical analyzed the data. MR, MT and MYA wrote introduction section of the manuscript. MR, BA and MT wrote methodology section of the manuscript. MR, BA, AMS and MA wrote results and discussion section of the manuscript.
Drought is one of the major abiotic threat to rice production in the context of climate change. S... more Drought is one of the major abiotic threat to rice production in the context of climate change. Super Basmati is an elite, fine grain basmati rice variety grown in Punjab, Pakistan. Due to drought sensitive in nature, its yield has been facing an alarming situation in production because of gradual decrease in irrigated water for a couple of years. Three reported novel QTLs for drought tolerance were selected for incorporation into Super Basmati by employing marker assisted selection strategy. IR55419-04 with novel QTLs was used as a donor parent. Foreground selection was performed by applying PCR based QTL linked SSR markers followed by recombinant selection by using 2-4 flanking markers. Background selection was exercised by using polymorphic SSR markers for maximum genome recovery of the Super Basmati. The individuals homozygous at the target QTLs and with maximum background of Super Basmati at the rest of the non-target genome was selected for evaluation of drought tolerance. Under drought stress conditions, the yields of all introgressed lines (ILs) were 44.2%-125.7% higher than recurrent parent. Six superior ILs that are drought tolerant and very similar to Super Basmati in terms of agronomic and grain quality traits are marked for release as drought-tolerant varieties in arid regions or for use in breeding programs of high grain quality and drought-tolerant parents.
R ice (Oryza sativa L.) is a staple food crop of more than half of the inhabitants across the glo... more R ice (Oryza sativa L.) is a staple food crop of more than half of the inhabitants across the globe (Khush, 2004). In Pakistan, after wheat, it occupies 2 nd position. Its cropped area was 3034 M ha and production was 7.410 M tons (Economic Survey of Pakistan, 2019). Among the cereal crops, rice is an important export commodity (Economic Survey of Pakistan, 2019). It contributes 3.1% in value addition to agriculture and 0.6% in the GDP (Economic Survey of Pakistan, 2019). The average yield of rice in Pakistan is about 2.44 t ha -1 (Economic Survey of Pakistan, 2019) which is low as compared to other rice producing countries due to many constraints including proper crop establishing techniques . In Asia rice is growing by transplanting, rice seedlings manually in puddled soil which is a widely adopted method. It consumes abundant water . Whereas, water resources are declining day by day. Its judicious use is gaining a pivotal importance to fulfil future water and food demand for the growing population . Shrinking water resources availability is a threat for the future rice production in Asia and will adversely affect the sustainability of Abstract | Planting method is an important aspect of production technology for the maximum resource utilization by crops per unit area. Dry-seeded rice (DSR) is a contemporary resource saving crop establishing technique, which enables farmers to harvest economical rice production. Field study was conducted at Rice Research Institute, Kala Shah Kaku, Pakistan in 2014 and in 2015 to evaluate the different planting methods. Three dry-seeded rice (DSR) planting methods viz. (i) DSR-broadcast, (ii) DSR-drill, (iii) DSR-ridges were compared with the conventional transplanting (TR) method in lines having row to row and plant to plant distance of 22.5cm distance, and farmer transplanting method. Experimental design was randomized complete block, replicated 3 times. Data were recorded on height (cm), tillers m -2 , filled and unfilled grains panicle -1 , thousand grain weight (g), grain and biomass yield (t ha -1 ). Grain sterility (%) and harvest index (%) were also calculated. Highest grain yield (5.00 to 5.11 t ha -1 ) with harvest index (30.00 to 31.50%) and relatively low grain sterility (12.00 to 12.01%) were observed in DSR-ridge and DSR-drill sowing method. Moreover, DSR (i.e. DSR-ridge and -drill) resulted in 104 and 76 % more profit over TR-farmer practice. The study concluded that DSR-ridge and DSR-drill proved to be the best to obtain the maximum paddy yield and net profit. Farmers can adopt these methods to harvest maximum benefit.
Sogatella furcifera Horvath and brown planthopper (BPH) Nilaparvata lugens Stål. Rice planthopper... more Sogatella furcifera Horvath and brown planthopper (BPH) Nilaparvata lugens Stål. Rice planthoppers are considered as severe and notorious insect pests of rice crop (Sabir et al., 2016). These planthoppers have also achieved the status of most destructive pests in rice crop (
Rice holds the key to future food security. In rice-growing areas, temperature has already reache... more Rice holds the key to future food security. In rice-growing areas, temperature has already reached an optimum level for growth, hence, any further increase due to global climate change could significantly reduce rice yield. Several mapping studies have identified a plethora of reproductive tissue-specific and heat stress associated inconsistent quantitative trait loci (QTL), which could be exploited for improvement of heat tolerance. In this study, we performed a meta-analysis on previously reported QTLs and identified 35 most consistent meta-QTLs (MQTLs) across diverse genetic backgrounds and environments. Genetic and physical intervals of nearly 66% MQTLs were narrower than 5 cM and 2 Mb respectively, indicating hotspot genomic regions for heat tolerance. Comparative analyses of MQTLs underlying genes with microarray and RNA-seq based transcriptomic data sets revealed a core set of 45 heat-responsive genes, among which 24 were reproductive tissue-specific and have not been studied...
Rice is critical for sustainable food and nutritional security; however, nominal micronutrient qu... more Rice is critical for sustainable food and nutritional security; however, nominal micronutrient quantities in grains aggravate malnutrition in rice-eating poor populations. Here, we assessed genetic diversity in grain iron (Fe) and zinc (Zn) contents using trait-linked simple sequence repeat (SSR) markers in 56 fine and coarse grain rice accessions of different geographical origin. Aromatic fine gain accessions contained relatively higher Fe and Zn contents in brown rice (BR) than coarse grain accessions. Genotyping with 24 SSR markers identified 21 polymorphic markers, among which seventeen demonstrated higher gene diversity and polymorphism information content (PIC) values, strongly indicating that markers used in current research were moderate to highly informative for evaluating genetic diversity. Population structure, principal coordinate and phylogenetic analyses classified studied rice accessions into two fine grain specific and one fine and coarse grain admixture subpopulatio...
Basmati rice is treated as one of the world’s best rice due to its extra-long grain and unique ar... more Basmati rice is treated as one of the world’s best rice due to its extra-long grain and unique aroma,. Over the last decade, Pakistan has earned more than US$2 billion through basmati export. Unfortunately, basmati rice is being threatened with bacterial leaf blight (BLB) disease that leads to poor production and quality. We attempted pyramiding of BLB genes through marker-assisted backcross breeding using Super Basmati as the recipient and IRBB60 as the donor parent. BLB resistance genes Xa4, xa5, and Xa21 were used for introgression. Molecular markers MP1 and MP2, RM122, and pTA248 were used for Xa4, xa5, and Xa21 genes respectively for foreground selection. The 85 SSR polymorphic molecular markers were used for background selection, which showed a more than 90% recurrent parent genome recovery. Phenotypic traits for grain dimensions were also considered while selecting backcross female parents from BC1F1 to BC5F1, which resulted in saving the resources from background selection before the selfing of backcrossed lines. Multiple lines carrying BLB resistance genes combinations Xa4 + xa5 and Xa4 + xa5 + Xa21 were developed. The BC5F4 uniform lines showed resistance against BLB disease at hotspot locations. One of the developed lines, PKBB15–116, which has a yield advantage of more than 10%, tolerant to lodging, and has basmati quality. These pyramided lines in basmati background will also be helpful for breeders to incorporate resistance genes in a shorter period of time, in order to develop new basmati rice varieties in future.
Biofortification of staple crops with essential micronutrients is the sustainable way to overcome... more Biofortification of staple crops with essential micronutrients is the sustainable way to overcome the hidden hunger. A large number of quantitative trait loci (QTL) linked with grain micronutrient contents have been reported in different mapping studies. Identification of consistent QTLs across diverse genetic backgrounds is useful for candidate gene analysis and marker assisted selection of target traits. In this study, an up to date meta-analysis of grain iron and zinc associated QTLs was performed and 48 meta-QTLs (MQTLs) distributed across 12 rice chromosomes were identified. The 95% confidence intervals of identified genomic regions were significantly narrower than the average of their corresponding original QTLs. A total of 9308 genes/transcripts physically located within or near MQTL regions were retrieved and through prioritization of candidate genes (CGs) 663 non-redundant iron and zinc CGs were selected and studied in detailed. Several functionally characterized iron and zinc homoeostasis related genes e.g OsATM3, OsDMAS1, OsFRO2, OsNAS1-3, OsVIT2, OsYSL16, OsZIP3 and OsZIP7 were also included in our MQTL analysis. More than 64% genes were enriched with zinc and iron binding gene ontology terms and were involved in oxidation reduction process, carbohydrate metabolic process, regulation of transcription, trans-membrane transport, response to oxidative stress, cell redox homeostasis and proteolysis etc. In-silico transcriptomic analysis of rice identified 260 CGs which were regulated in response to iron and zinc stresses. We also identified at least 37 genes which were differentially expressed under both stress conditions and majority of these have not been studied in detailed before. Our results strongly indicate that majority of the MQTLs identified in this study are hotspots for grain iron and zinc concentration and are worth of intensive functional studies in near future.
Rice is food for more than half of the world population and the most consumable cereal in most of... more 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.
Journal of Experimental Biology and Agricultural Sciences, 2019
Rice is the staple food for half of the world"s population, however, its edible grain part is def... more Rice is the staple food for half of the world"s population, however, its edible grain part is deficient in essential micronutrients, especially Fe and Zn. Breeding for micronutrient dense rice demands exploration of available genetic diversity for grain Fe, Zn and β-carotene contents. In this study, we analysed brown and polished grain samples of 26 traditional rice genotypes for Fe and Zn concentration. Fe concentration varied from 13.23 ppm to 45.83 ppm and 1.10 ppm to 36.45 ppm in brown and polished rice, respectively. Whereas, Zn concentration in brown and polished rice ranged from 18.67 ppm to 38.01 ppm and 5.86 ppm to 23.88 ppm, respectively. The landraces had higher Fe and Zn contents than improved varieties and advance uniform lines. Significant positive correlation was present between Fe and Zn concentration in brown (r = 0.694, P < 0.01) and polished rice (r = 0.533, P < 0.01). Fe concentration was greatly reduced by the polishing process than Zn concentration and approved varieties lost less Fe and Zn contents than advance uniform lines. Minimal levels of beta-carotene were detected in rice genotypes indicating need for genetic modifications to enhance pro-vitamin A contents in rice endosperm.
Xanthomonas oryzae pv. oryzae (Xoo) has now become one of major rice diseases. During recent year... more Xanthomonas oryzae pv. oryzae (Xoo) has now become one of major rice diseases. During recent years, its occurrence has increased in Pakistan, particularly in 'Kallar tract' which is well-known for quality rice cultivation. Development of new resistant varieties by utilizing the available resistant gene-pool is most reliable breeding technique for the plant breeders. The present study was conducted to explore the genetic resources regarding presence and absence of BLB resistance genes Xa4, xa5 and Xa21 through DNA marker technology. Effectiveness of Xa21 followed by xa5 and Xa7 genes has been reported to confer more resistance level for BLB in traditional rice belt of Pakistan. For this purpose, eighty (80) rice genotypes comprising of diverse origin including three isogenic lines viz., IRBB4 (carrying Xa4), IRBB5 (carrying xa5) and IRBB21 (carrying Xa21) as positive resistant gene checks and IR24 (carrying none of these) as negative gene check were genotyped. DNA fingerprinting results indicated the presence of Xa4 gene in 41 entries, while 14 lines were positive for xa5 gene. Only one local line was carrying Xa21 gene along with Xa4. Thus, the present study will not only be helpful for rice breeders to develop new rice varieties carrying disease resistant genes, but will also provide the donors to incorporate / pyramid disease resistant genes in popular rice varieties like Super Basmati and Basmati 515 which are susceptible to BLB disease.
Chemical mutagens have long been used to create genetic variability in crop plants for breeding r... more Chemical mutagens have long been used to create genetic variability in crop plants for breeding research and genetic studies. In rice, more than 500 varieties have been released through induced mutations. Ethyl methane sulphonate (EMS) is the most commonly used chemical mutagen in plants. EMS normally induces Gas chromatography GC to AT transitions in the genome and thus resulting protein in the mutant plant has different functions than normal. The present study was carried out to investigate the mutagenic effects of different concentrations of EMS on germination and yield parameters of two basmati rice cultivars (Super basmati and Basmati 370). The seeds were subjected to different treatment levels of EMS. The treated and untreated plants were observed under different agronomic parameters. EMS was quite effective in inducing genetic variability in Basmati rice. The results revealed significant difference among all the traits studied. The efficiency of EMS was found to depend upon its concentration and it was higher at lower concentration in both genotypes. The study further revealed that the use of EMS is an effective approach for creating new rice germplasm.
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Papers by Muhammad Sabar