A review on gene pyramiding of agronomic, biotic and abiotic traits in rice variety development

Rice Oryza sativa L is a staple food crop, and its seeds are the most important component part of the agronomic trait of the cereal crop, rich in nutrient and of economic value to human and even livestock. But, it is often threatened by various abiotic and biotic conditions that reduce the yield, because of high incidences of infectious disease agents and non-pathogenic conditions respectively. Pyramiding of the requisite resistance and tolerance genes into single elite high yielding variety of rice, confers wider spectrum of stress management, resulting to development of single multiline variety of rice. Marker-assisted selection utilizes DNA marker-linked primers for blast resistant gene (RM8225;Piz, RM6836;Piz, Pi2,Pi9), bacteria leaf blight (RM224; Xa-4, RM122;xa-5, RG136; xa-13, RM21;Xa-21) and drought tolerance (RM236;qDTY2.2, RM520;qDTY3.1, RM511;qDTY12.1) in pedigree, backcross and recurrent selection breeding methods. The objectives are to create awareness on the environmental safety of host-resistance, significance of single multiline resistance variety, effect of the interaction of stress conditions and associated simple sequence repeat (SSR) linked markers

Genetic diversity and utilization of cultivated eggplant germplasm in varietal improvement

Eggplant is the fifth economically most important vegetable in the Solanaceae family after tomato, potato, chili, and tobacco. Apart from the well-cultivated brinjal or aubergine eggplant (Solanum melongena L.), two other underutilized eggplant species, the African eggplant (S. macrocarpon L.) and the scarlet eggplant (S. aethiopicum L.), were also cultivated with local importance where the leaves and fruits are used for food and medicinal purposes. The major objectives of the eggplant breeding program are to improve fruit quality, increase yield performance through heterosis breeding, and introduce pest and disease resistances from wild relatives. Europe and Asia hold a wide collection of germplasm resources with significant potential for genetic improvement. While cultivated eggplant is susceptible to several fungi and bacteria, many wild relatives offer potential resistance to these pathogens. In this paper, we review the genetic resources and diversity of cultivated eggplant and its wild relatives. As a point of departure, we examine the economic importance, domestication, taxonomy characterization, and relationships of the crop and its wild relatives. The importance of evaluating and safeguarding wild relatives is highlighted, as crop wild relatives are highly underrepresented. A key section in this study is an overview dedicated to genetic resources, resistance to biotic and abiotic stresses, pre-breeding, and breeding for sustainable eggplant production

Genetic diversity and variability among pigmented rice germplasm using molecular marker and morphological traits

Exploring the genetic aspects of germplasm using genotypic and phenotypic analysis is more reliable for the development of rice varieties that could lead to the attainment of food security. This is because genetic variations provide a space for recombinants, which is an important factor in new varietal development. This study was conducted to evaluate genetic variability and diversity among 32 coloured rice accessions using agro-morphological characteristics and simple sequence repeats (SSR) markers. Quantitative traits (morphological, grain quality and antioxidant properties) and 34 SSR molecular markers were used as tools for determining cultivar identities and genetic diversity. Most of the quantitative traits showed significant differences (p ≤ 0.01) among all rice accessions. Clustering analysis from quantitative traits categorised the accessions into four groups. Similarly, the 32 accessions were grouped into 4 cluster groups based on the analysis of 34 SSR markers. The accessions YTM15, Pulut Merah 3, Padi Randau, Ringan Bawang, DNJ128 and DV 107 can be potentially selected for development of new varieties for local cultivation. Finally, these accessions can be used as parents in further breeding programmes

Bacterial leaf blight resistance in rice: a review of conventional breeding to molecular approach

Breeding for disease resistant varieties remains very effective and economical in controlling the bacterial leaf blight (BLB) of rice. Breeders have played a major role in developing resistant rice varieties against the BLB infection which has been adjudged to be a major disease causing significant yield reduction in rice. It would be difficult to select rice crops with multiple genes of resistance using the conventional approach alone. This is due to masking effect of genes including epistasis. In addition, conventional breeding takes a lot of time before a gene of interest can be introgressed. Linkage drag is also a major challenge in conventional approach. Molecular breeding involving markers has facilitated the characterization and introgression of BLB disease resistance genes. Biotechnology has brought another innovation in form of genetic engineering (transgenesis) of rice. Although, molecular breeding cannot be taken as a substitute for conventional breeding, molecular approach for combating BLB disease in rice is worthwhile given the demand for increased production of rice in a fast growing population of our society. This present article highlights the recent progress from conventional to molecular approach in breeding for BLB disease resistant rice varieties

Development of high yielding, bacterial leaf blight and blast disease resistant rice (Oryza sativa L.) variety through marker-assisted backcross breeding

Rice is an important food crop that serves as a major carbohydrate source for nearly half of the world’s population. Bacteria leaf blight caused by the pathogen Xanthomonas oryzae pv. oryzae (Xoo) is one of the most serious diseases responsible for significant yield reduction in rice. Rice blast disease is caused by the fungal pathogen Magnaporthe oryzae. Both are very destructive diseases of rice in Malaysia and other parts of the world’s major rice growing regions causing considerable yield loss. The main objective of this study was to develop high yielding, bacterial leaf blight and blast disease resistant rice variety for commercial cultivation in Malaysia through marker-assisted backcross breeding. Parental varieties used were Putra-1 which is high yielding and blast resistant, and served as the recipient, and IRRB60 as the donor which is bacterial leaf blight resistant. Fifteen simple sequence repeats (SSR) and functional markers that were reported to be linked to Xoo resistance genes were screened to confirm their polymorphism between the two parents. Also, two SSR DNA-based markers that are linked to blast resistance genes were tested for their polymorphism between the two parents. A total of 472 rice SSR markers were screened out of which 79 polymorphic markers were identified between the two parents. A total of 16.74% level of polymorphism spread across the 12 rice chromosomes was recorded from the 472 markers assessed. The result showed that the number of polymorphic markers per chromosome confirmed ranged from four (chromosomes 10 and 11) to nine (chromosomes 2, 8 and 12). Out of the 72 grown F1 plants, five F1 hybrids were confirmed to carry all the Xoo (Xa21, xa13, xa5, Xa4) and blast (Piz, Pi2 and Pi9) resistance genes. These five progenies were selected for use in the next crossing to produce BC1F1 population. A total of 288 BC1F1 progenies were obtained from a cross between the best F1 progeny and Putra-1. The Chi-square (χ²) result of the six foreground markers segregation analysis showed no significant difference in the BC1F1 progenies from a 1:1 Mendelian segregation ratio. The result indicated a goodness of fit to the single gene model. The mean recurrent parent genome recovery (RPGR) of BC1F1 population was 80.11%. The best progeny in BC1F1 population was BC1F1-38, with the RPGR of 86.40% and the low heterozygous component of 8.70% and reduced donor genome of 4.90%, in addition to very negligible linkage drag. Out of 268 BC2F1 progenies, 14 plants were confirmed to carry all the seven Xoo and blast resistance genes while χ² result of foreground marker segregation showed a goodness of fit to the single gene model. With the result obtained on recurrent parent genome recovery from marker- assisted background selection of BC2F1 after genotyping, coupled with further confirmation through phenotyping, nine best BC2F1 progenies with recurrent parent genome recovery of more than 95.31% were selected. A total of 220 BC2F2 progenies were grown from the nine selected recurrent parent genome recovered BC2F1 lines and furthermore, the final selection was made from homozygous individuals carrying the donor (IRBB60) parent allele with highest recurrent parent genome recovery percentage. The average RPGR recorded at BC2F2 was approximately 96%. Sixteen progenies from the BC2F2 generation were selected as advanced backcross lines. In the F1 progeny, percentage infection recorded ranged from 4.24% to 10.91%. The average percentage infection was 6.35% while the mean disease score was recorded as 1.00. This result showed that the Xoo resistance genes were introgressed into the F1 progenies and as such, resistant to bacterial leaf blight infection. The Xoo and blast resistance genes were re- validated in BC2F2 populations and the selected improved lines proved to be resistant to bacterial leaf blight and blast diseases. The selection using polymorphic tightly linked functional and SSR foreground markers was successfully used to identify BC1F1, BC2F1 and BC2F2 progenies with the targeted alleles. The introgression of dominant (Xa21, Xa4) and recessive (xa13, xa5) Xoo resistance genes as well as blast R-genes (Pi9, Pi2, Piz) were confirmed in the selected BC1F1, BC2F1 and BC2F2 progenies. The high percentage of recurrent parent genome recovery in these populations was an indication of high potentials of marker-assisted backcross breeding in recovering the genomes of the recurrent parent in rice and other cereal crops. The successful pyramiding of seven Xoo and blast resistance genes in the newly developed rice lines will guarantee a broad spectrum and durable resistance. This breeding programme is the very first successful attempt to manipulate the genome of the Malaysian elite rice variety Putra-1 without jeopardising its high yielding characteristic and blast resistance but with additional advantage of Xoo resistance in the newly improved lines. The newly developed rice lines are recommended varieties suitable for commercial cultivation in Malaysia and other rice growing regions

Submergence tolerance in rice: review of mechanism, breeding and, future prospects

Flooding or submergence is one of the major environmental stressors affecting many man-made and natural ecosystems worldwide. The increase in the frequency and duration of heavy rainfall due to climate change has negatively affected plant growth and development, which eventually causes the death of plants if it persists for days. Most crops, especially rice, being a semi-aquatic plant, are greatly affected by flooding, leading to yield losses each year. Genetic variability in the plant response to flooding includes the quiescence scheme, which allows underwater endurance of a prolonged period, escape strategy through stem elongation, and alterations in plant architecture and metabolism. Investigating the mechanism for flooding survival in wild species and modern rice has yielded significant insight into developmental, physiological, and molecular strategies for submergence and waterlogging survival. Significant progress in the breeding of submergence tolerant rice varieties has been made during the last decade following the successful identification and mapping of a quantitative trait locus for submergence tolerance, designated as SUBMERGENCE 1 (SUB1) from the FR13A landrace. Using marker-assisted backcrossing, the SUB1 QTL (quantitative trait locus) has been incorporated into many elite varieties within a short time and with high precision as compared with conventional breeding methods. Despite the advancement in submergence tolerance, for future studies, there is a need for practical approaches exploring genome-wide association studies (GWA) and QTL in combination with specific tolerance traits, such as drought, salinity, disease and insect resistance

Genotypic and phenotypic relationship among yield components in rice under tropical conditions

The associations among yield-related traits and the pattern of influence on rice grain yield were investigated. This evaluation is important to determine the direct and indirect effects of various traits on yield to determine selection criteria for higher grain yield. Fifteen rice genotypes were evaluated under tropical condition at five locations in two planting seasons. The experiment was laid out in a randomized complete block design with three replications across the locations. Data were collected on vegetative and yield components traits. The pooled data based on the analysis of variance revealed that there were significant differences (p<0.001) among the fifteen genotypes for all the characters studied except for panicle length and 100-grain weight. Highly significant and positive correlations at phenotypic level were observed in grain weight per hill (0.796), filled grains per panicle (0.702), panicles per hill (0.632), and tillers per hill (0.712) with yield per hectare, while moderate positive correlations were observed in flag leaf length to width ratio (0.348), days to flowering (0.412), and days to maturity (0.544). By contrast, unfilled grains per panicle (-0.225) and plant height (-0.342) had a negative significant association with yield per hectare. Filled grains per panicle (0.491) exhibited the maximum positive direct effect on yield followed by grain weight per hill (0.449), while unfilled grain per panicle (-0.144) had a negative direct effect. The maximum indirect effect on yield per hectare was recorded by the tillers per hill through the panicles per hill. Therefore, tillers per hill, filled grains per panicle, and grain weight per hill could be used as selection criteria for improving grain yield in rice

Drought resistance in rice from conventional to molecular breeding: a review

Drought is the leading threat to agricultural food production, especially in the cultivation of rice, a semi-aquatic plant. Drought tolerance is a complex quantitative trait with a complicated phenotype that affects different developmental stages in plants. The level of susceptibility or tolerance of rice to several drought conditions is coordinated by the action of different drought-responsive genes in relation with other stress components which stimulate signal transduction pathways. Interdisciplinary researchers have broken the complex mechanism of plant tolerance using various methods such as genetic engineering or marker-assisted selection to develop a new cultivar with improved drought resistance. The main objectives of this review were to highlight the current method of developing a durable drought-resistant rice variety through conventional breeding and the use of biotechnological tools and to comprehensively review the available information on drought-resistant genes, QTL analysis, gene transformation and marker-assisted selection. The response, indicators, causes, and adaptation processes to the drought stress were discussed in the review. Overall, this review provides a systemic glimpse of breeding methods from conventional to the latest innovation in molecular development of drought-tolerant rice variety. This information could serve as guidance for researchers and rice breeders

Superabsorbent polymer hydrogels for sustainable agriculture: a review

Water management is rapidly becoming one of the most pressing issues facing all countries in semi-arid and arid parts of the world. Global water consumption is predicted to increase by 50% in 2030, resulting in an acute water shortage. Presently, the agricultural sector consumes more than 70% of freshwater in most regions of the world, putting more pressure on water scarcity. Hydrogels are superabsorbent polymers that can hold plant nutrients and water when the soil around plant roots starts to dry out. Research evidence has revealed that water stored by hydrogel slowly returns to the soil, thereby increasing the volumetric water content of the soil. Hydrogel increases water use efficiency and irrigation intervals, decreases irrigation costs, and provides plants with the required nutrients and moisture. Numerous properties of hydrogels, including moderate water retention and high swelling, make them ideal as a safe delivery mechanism in agriculture for soil conditioners and agents for the controlled release of fertilizers. Numerous research publications on hydrogel polymer synthesis and its characteristics have been published. However, the current review emphasizes the critical role of superabsorbent hydrogels in an integrated approach for the balanced protection of seeds, plants, and soil to conserve the ecosystem

Marker-assisted introgression of multiple resistance genes confers broad spectrum resistance against bacterial leaf blight and blast diseases in Putra-1 rice variety

Bacterial leaf blight caused by Xanthomonas oryzae pv oryzae (Xoo) and blast caused by Magnaporthe oryzae are major diseases responsible for significant yield loss in rice production across all rice growing regions. Host plant resistance has been advocated as a sustainable means of guarding against the diseases. This experiment was conducted with the aim to introgress multiple resistance genes against bacterial leaf blight and blast diseases through marker-assisted backcross breeding. Two dominant (Xa4 and Xa21) and two recessive (xa5 and xa13) Xoo resistance genes were introgressed into a high yielding Malaysian rice variety Putra-1 with genetic background of three blast resistance (Piz, Pi2 and Pi9) genes. Eight polymorphic tightly linked functional and SSR markers were used for foreground selection of target genes. Seventy nine polymorphic SSR markers were used in background selection. The plants were challenged at initial stage of breeding and challenged again at BC2F2 with the most virulent Malaysian pathotypes of Xoo (P7.7) and Magnaporthe oryzae (P7.2) to test their resistance. Results obtained from foreground marker segregation analysis at BC1F1 and BC2F1 showed that the marker polymorphism both fitted into the Mendel’s single gene segregation ratio of 1:1 for both Xoo and blast resistance. At BC2F2, results indicated that foreground marker polymorphism fitted into the expected Mendelian ratio of 1:2:1 for blast resistance only. Marker-assisted background selection revealed high percentage of recurrent parent genome recovery (95.9%). It was concluded that the inheritance of blast resistance in the introgressed lines was mainly due to single gene action while the inheritance of Xoo resistance was substantially due to single nuclear gene action. The incorporation of four bacterial leaf blight and three blast resistance genes (Xa4 + xa5 + xa13 + Xa21; Pi9 + Pi2 + Piz) in the newly developed lines would provide for broad spectrum and durable resistance against the two major diseases studied