High kernel elongation (HKE) is one of the high-quality characteristics in rice. The objectives of this study were to determine the effects of ageing treatments, gene actions, and inheritance pattern of kernel elongation on cooking quality in two populations of rice and determine the path of influence and contribution of other traits to kernel elongation in rice. Two rice populations derived from crosses between MR219 × Mahsuri Mutan and MR219 × Basmati 370 were used. The breeding materials included two F1 progenies from the two populations, and their respective parents were grown in four different batches at a week interval to synchronize the flowering between the female and male plants. Scaling tests and generation means analysis were carried out to determine ageing effects and estimate additive-dominance gene action and epistasis. The estimation of gene interaction was based on quantitative traits. Path coefficient analysis was done using SAS software version 9.4 to determine the path of influence (direct or indirect) of six quantitative traits on HKE. Results obtained showed that nonallelic gene interaction was observed in all traits. The results before ageing and after ageing showed significant differences in all traits, while the gene interaction changed after ageing. The HKE value improved after ageing, suggesting that ageing is an external factor that could influence gene expression. The epistasis effect for HKE obtained from the cross Mahsuri Mutan × MR219 showed duplicate epistasis while that obtained from a cross between Basmati 370 × MR219 showed complimentary epistasis. Besides, the heritability of HKE was higher in Basmati 370 × MR219 compared to that obtained in Mahsuri Mutan × MR219. The path analysis showed that the cooked grain length and length-width ratio positively significantly affected HKE. It was concluded that ageing treatment is an external factor that could improve the expression of HKE. The findings from this study would be useful to breeders in the selection and development of new specialty (HKE) rice varieties.
The trend of microsatellite marker discovery and development revolved as a result of the advancement of next generation sequencing (NGS) technology as it has developed numerous microsatellites within a short period of time at a low cost. This study generated microsatellite markers using RAD sequencing technologies for the understudied Nephelium lappaceum. A total of 1403 microsatellite markers were successfully designed, which consisted of 853 di-, 525 tri-, 17 tetra-, 5 penta-, and 3 hexanucleotide microsatellite markers. Subsequently, selection of 39 microsatellites was made for the evaluation of genetic diversity of the selected 22 rambutan varieties. Twelve microsatellites, which exhibited high call rates across the samples, were used to assess the diversity of the aforementioned rambutan varieties. The analysis of 12 microsatellites revealed the presence of 72 alleles and six alleles per locus in average. Furthermore, the polymorphic information content (PIC) value ranged from 0.326 (NlaSSR20) to 0.832 (NlaSSR32), which included an average of 0.629 per locus, while the generated Neighbour Joining dendrogram showed two major clusters. The pairwise genetic distance of shared alleles exhibited a range of values from 0.046 (R134↔R170) to 0.818 (R5↔R170), which suggested highest dissimilarity detected between R5 and R170. Notably, these research findings would useful for varietal identification, proper management and conservation of the genetic resources, and exploitation and utilization in future breeding programs.
Agriculture is now facing the 'perfect storm' of climate change, increasing costs of fertilizer and rising food demands from a larger and wealthier human population. These factors point to a global food deficit unless the efficiency and resilience of crop production is increased. The intensification of agriculture has focused on improving production under optimized conditions, with significant agronomic inputs. Furthermore, the intensive cultivation of a limited number of crops has drastically narrowed the number of plant species humans rely on. A new agricultural paradigm is required, reducing dependence on high inputs and increasing crop diversity, yield stability and environmental resilience. Genomics offers unprecedented opportunities to increase crop yield, quality and stability of production through advanced breeding strategies, enhancing the resilience of major crops to climate variability, and increasing the productivity and range of minor crops to diversify the food supply. Here we review the state of the art of genomic-assisted breeding for the most important staples that feed the world, and how to use and adapt such genomic tools to accelerate development of both major and minor crops with desired traits that enhance adaptation to, or mitigate the effects of climate change.
Hevea brasiliensis is exploited for its latex production, and it is the only viable source of natural rubber worldwide. The demand for natural rubber remains high due its high-quality properties, which synthetic rubber cannot compete with. In this paper, we present transcriptomic data and analysis of three H. brasiliensis clones using tissue from latex and bark tissues collected from 10-year-old plant. The combined, assembled transcripts were mapped onto an H. brasiliensis draft genome. Gene ontology analysis showed that the most abundant transcripts related to molecular functions, followed by biological processes and cellular components. Simple sequence repeats (SSR) and single nucleotide polymorphisms (SNP) were also identified, and these can be useful for selection of parental and new clones in a breeding program. Data generated by RNA sequencing were deposited in the NCBI public repository under accession number PRJNA629890.
Interspecific hybridization has been reported for a wide variety of vertebrate species either spontaneous or by organized crossing of bovine species. The hybrids were often carrying intermediate characters genetically and phenotypically of the parents. Thus, status information of both aspects is valuable in animal production for selection and breeding management. The Gaur-cattle hybrids was reported to be superior in production value compared to their parent cattle but fertility status was still questionable. The project was abandoned due to their fertility issue and the hybrids were kept within the cattle in a dairy farm. Cytogenetic status and breeding record of the remaining herd were unavailable since then. The herd was then translocated to a deer farm (PTH Lenggong) and kept freely in the paddock. Recently, two female calves were born via inter se mating. Peripheral blood cultures of Malayan Gaur, Sahiwal-Friesian cattle and Gaur x cattle hybrid backcrosses were analyzed via Giemsa stained metaphase. The Gaur and cattle were having diploid chromosome number (2n) of 56 and 60, respectively. Interestingly, the backcrosses from the hybrids by cattle bulls were found to have two chromosome arrangements, which are 2n = 58 and 2n = 60.
Restriction fragment length polymorphism and virulence analyses were used to evaluate the population structure of Xanthomonas oryzae pv. oryzae, the rice bacterial blight pathogen, from several rice-growing countries in Asia. Two DNA sequences from X. oryzae pv. oryzae, IS1112, an insertion sequence, and avrXa10, a member of a family of avirulence genes, were used as probes to analyze the genomes of 308 strains of X. oryzae pv. oryzae collected from China, India, Indonesia, Korea, Malaysia, Nepal, and the Philippines. On the basis of the consensus of three clustering statistics, the collection formed five clusters. Genetic distances within the five clusters ranged from 0.16 to 0.51, and distances between clusters ranged from 0.48 to 0.64. Three of the five clusters consisted of strains from a single country. Strains within two clusters, however, were found in more than one country, suggesting patterns of movement of the pathogen. The pathotype of X. oryzae pv. oryzae was determined for 226 strains by inoculating five rice differential cultivars. More than one pathotype was associated with each cluster; however, some pathotypes were associated with only one cluster. Most strains from South Asia (Nepal and India) were virulent to cultivars containing the bacterial blight resistance gene xa-5, while most strains from other countries were avirulent to xa-5. The regional differentiation of clusters of X. oryzae pv. oryzae in Asia and the association of some pathotypes of X. oryzae pv. oryzae with single clusters suggested that strategies that target regional resistance breeding and gene deployment are feasible.
Robustness has become a highly desirable breeding goal in the globalized agricultural market. Both genotype-by-environment interaction (G × E) and micro-environmental sensitivity are important robustness components of aquaculture production, in which breeding stock is often disseminated to different environments. The objectives of this study were (i) to quantify the degree of G × E by assessing the growth performance of Genetically Improved Farmed Tilapia (GIFT) across three countries (Malaysia, India and China) and (ii) to quantify the genetic heterogeneity of environmental variance for body weight at harvest (BW) in GIFT as a measure of micro-environmental sensitivity. Selection for BW was carried out for 13 generations in Malaysia. Subsets of 60 full-sib families from Malaysia were sent to China and India after five and nine generations respectively. First, a multi-trait animal model was used to analyse the BW in different countries as different traits. The results indicate a strong G × E. Second, a genetically structured environmental variance model, implemented using Bayesian inference, was used to analyse micro-environmental sensitivity of BW in each country. The analysis revealed the presence of genetic heterogeneity of both BW and its environmental variance in all environments. The presence of genetic variation in residual variance of BW implies that the residual variance can be modified by selection. Incorporating both G × E and micro-environmental sensitivity information may help in selecting robust genotypes with high performance across environments and resilience to environmental fluctuations.
Although indigenous climbing perch (Anabas testudineusis) is a highly valuable species, slow growth pattern during the culture period impeding its commercial success in aquaculture. In many fish species, it has been demonstrated that incubation temperature of eggs influenced the muscle development and growth rates, which persisted throughout the subsequent larval and juvenile phases. Therefore, this study aimed to investigate whether different incubation temperature of eggs prior to hatching can stimulate the muscle development, growth, and growth-related gene expression of the slow-growing indigenous species of climbing perch. The fertilized eggs of A. testudineus from an artificial breeding program were incubated under control temperature of 24 °C (IT24), 26 °C (IT26), 28 °C (IT28), and 30 °C (IT30) in 10L glass aquaria with four replicated units for each temperature treatment. After hatching, the larvae from each incubated temperature were separately reared at ambient temperature for 10 days in aquarium, 20 days in hapas, and the next 42 days in cages, totaling 72 days post-hatching (dph). The hatching rates were found significantly (P
The contamination of aquaculture products and effluents by contaminants of emerging concern (CECs) from the direct chemical use in aquaculture activities or surrounding industries is currently an issue of increasing concern as these CECs exert acute and chronic effects on living organisms. CECs have been detected in aquaculture water, sediment, and culture species, and antibiotics, antifoulants, and disinfectants are the commonly detected groups. Through accumulation, CECs can reside in the tissue of aquaculture products and eventually consumed by humans. Currently, effluents containing CECs are discharged to the surrounding environment while producing sediments that eventually contaminate rivers as receiving bodies. The rearing (grow-out) stages of aquaculture activities are issues regarding CECs-contamination in aquaculture covering water, sediment, and aquaculture products. Proper regulations should be imposed on all aquaculturists to control chemical usage and ensure compliance to guidelines for appropriate effluent treatment. Several techniques for treating aquaculture effluents contaminated by CECs have been explored, including adsorption, wetland construction, photocatalysis, filtration, sludge activation, and sedimentation. The challenges imposed by CECs on aquaculture activities are discussed for the purpose of obtaining insights into current issues and providing future approaches for resolving associated problems. Stakeholders, such as researchers focusing on environment and aquaculture, are expected to benefit from the presented results in this article. In addition, the results may be useful in establishing aquaculture-related CECs regulations, assessing toxicity to living biota, and preventing pollution.
Megaselia scalaris (Loew) is one of the best-known diets for the swiftlet. Previous studies have addressed the problem of some mass rearing conditions for this insect; unfortunately, the details of the nutritional composition of the life stages and cost of the breeding materials were insufficiently reported, even though this information is crucial for farming the edible-nest swiftlet. We aimed to investigate the nutritional composition of the life stages of M scalaris on a cost basis using 3 common commercial breeding materials: chicken pellets (CPs), fish pellets (FPs), and mouse pellets (MPs). Modified Association of Official Analytical Chemists (AOAC) proximate and mineral analyses were carried out on the insect's third instar larvae, pupal, and adult stages to determine the nutritional composition. Regardless of the breeding materials, the adult stage of M scalaris had significantly higher crude protein than the other stages; the pupae were rich in calcium, which is required for egg production; and the third instar larvae had the highest amount of crude fat compared with the other stages. Regarding the energy content, there were no significant differences among the stages according to the breeding materials. In terms of nutritional cost, CP was the most economic breeding material and generated the highest amount of nutrients per US dollar (US $). Different life stages of M scalaris were used by the swiftlets by supplying the required nutrients, and future studies should focus on effective diet feeding methods.
Quality of planting materials determines future successes of plantations and subsequent endeavours in the life cycle. Oil palm (Elaeis guineensis) breeding triggered an industry in Malaysia through “Plant Introduction” with the establishment of the first oil palm plantation. At the wake of the oil palm industry, plantations utilised the dura planting material. The hallmark discovery of the single gene inheritance for shell thickness led to the prolific dura x pisifera (DxP) derived tenera planting material. Subsequent parental inbred lines developed in recurrent selections, crossed and progeny tested exploiting heterosis had boosted yields. Further improvements were foresighted and executed in the widening of the genetic pool and collections of germplasm in centres of origin/diversity in Africa and Latin America. Field Genebank of the Malaysian Palm Oil Board (MPOB) forms the world’s largest ex situ oil palm conservation programme. This programme enabled the developments of elite breeding populations harbouring specialty oils and products. Meanwhile, opening of large oil palm areas by the Federal Land Development Authority (Felda) set the momentum in rapid expansion of the industry. Felda is an exemplary in wealth creation and quality of life (QOL). Resettlements of landless farmers into Felda schemes, employing modern farming, mainly in oil palm has helped eradicate poverty and uplifting QOL among settlers, employees and their families. Impacts of the success in wealth creation and its distribution leading to better QOL, rooted from breeding through the supply of quality planting materials. Phenotypic expressions of the planting materials were realised through genotypic and environment interactions; the former through breeding, the latter through agronomic practices. Efforts in oil palm breeding helped paved the way to a mammoth industry, contributing to the nation economic growths, impacting livelihood of the people. Further progress in yield is expected from clones, where breeding has a role in the supply of quality ortets. Genetic potential of planting materials can be further exploited through interdisciplinary approach in breeding, biotechnology and genomics. With continuing wealth creation, the oil palm saga continues. Once wealth is created, QOL will follow.
Bambara groundnut (Vigna subterranea (L.) Verdc.) is an indigenous underutilized legume that has the potential to improve food security in semi-arid Africa. So far, there are a lack of reports of controlled breeding populations that could be used for variety development and genetic studies. We report here the construction of the first genetic linkage map of bambara groundnut using a F3 population derived from a "narrow" cross between two domesticated landraces (Tiga Nicuru and DipC) with marked divergence in phenotypic traits. The map consists of 238 DArT array and SSR based markers in 21 linkage groups with a total genetic distance of 608.3 cM. In addition, phenotypic traits were evaluated for a quantitative trait loci (QTL) analysis over two generations. A total of 36 significant QTLs were detected for 19 traits. The phenotypic effect explained by a single QTL ranged from 11.6% to 49.9%. Two stable QTLs were mapped for internode length and growth habit. The identified QTLs could be useful for marker-assisted selection in bambara groundnut breeding programmes.
The application of the Geographic Information Systems (GIS) to the study of vector transmitted diseases considerably improves the management of the information obtained from the field survey and facilitates the study of the distribution patterns of the vector species.
Submergence or flood is one of the major harmful abiotic stresses in the low-lying countries and crop losses due to waterlogging are considerably high. Plant breeding techniques, conventional or genetic engineering, might be an effective and economic way of developing crops to grow successfully in waterlogged condition. Marker assisted selection (MAS) is a new and more effective approach which can identify genomic regions of crops under stress, which could not be done previously. The discovery of comprehensive molecular linkage maps enables us to do the pyramiding of desirable traits to improve in submergence tolerance through MAS. However, because of genetic and environmental interaction, too many genes encoding a trait, and using undesirable populations the mapping of QTL was hampered to ensure proper growth and yield under waterlogged conditions Steady advances in the field of genomics and proteomics over the years will be helpful to increase the breeding programs which will help to accomplish a significant progress in the field crop variety development and also improvement in near future. Waterlogging response of soybean and major cereal crops, as rice, wheat, barley, and maize and discovery of QTL related with tolerance of waterlogging, development of resistant variety, and, in addition, future prospects have also been discussed.
Assessing performance and genetic diversity of the wild material of oil palm is important for
under- standing genetic structure of natural oil palm populations towards improvement of the
crops. This in-formation is important for oil palm breeding programs, and also for continued exsitu
conservation of the germplasm and breeding program in Malaysia. Mutation induction is one
of the approaches in creating variants for selection in the breeding program. In this study, the
effect of irradiated pollen towards pollen viability, bunches formation and number of
parthenocarpic fruits were evaluated. Elaies guineensis Jacq. pollens were exposed to series of
acute gamma radiation at dose 0, 10, 20, 40, 50, 100, 200, 300, 500, 100 and 2000 Gy . Pollen
viability and pollen tube formation were disrupted in which unable the pollen to reach the ovule.
At this stage, embryo was aborted towards formation of parthenocarpic fruits and rotten bunches.
The study suggested that at low levels of irradiation i.e. < 200 Gy, generative nucleus partially
damage and it is still maintaining capacity of fertilizing the egg cells for hybridization. It is
important for breeders in understanding this finding towards novel variants of oil palm via
mutation induction
A resistant variety with high yielding potential is key for increasing crop production to
fulfill the food requirement of the ever increasing world populations. Consequently, the aim of plant
breeders is to develop high yielding varieties or cultivars that are resistant or tolerant to specific
diseases or insects. For developing a resistant variety, it is enormously indispensable to incorporate or
introgress the specific resistant genes of that particular disease into the recipient. Suppression
subtractive hybridization (SSH) is a powerful technique for the identification of disease specific
differentially expressed genes that are expressed in a resistant or susceptible variety. This paper
presents a brief review on the SSH technique with examples focusing on the identification of the
wheat disease specific differentially expressed genes and their defense mechanisms against fungal
pathogens in global wheat cultivars. This review is helpful for wheat researchers for the updated
information on the SSH technique for the identification of differentially expressed genes in the global
wheat cultivars and varieties. Eventually, the identified genes could be used to develop the disease
resistance variety through marker-assisted backcrossing programme or conventional breeding.
Many of the most widely spread vector-borne diseases are water related, in that the mosquito vectors concerned breed or pass part of their lifecycle in or close to water. A major reason for the study of mosquito larval ecology is to gather information on environmental variables that may determine the species of mosquitoes and the distribution of larvae in the breeding habitats. Larval surveillance studies were conducted six times between May 2008 and October 2009 in Pos Lenjang, Kuala Lipis, Pahang. Twelve environmental variables were recorded for each sampling site, and samples of mosquito larvae were collected. Larval survey studies showed that anopheline and culicine larvae were collected from 79 and 67 breeding sites, respectively. All breeding sites were classified into nine habitat groups. Culicine larvae were found in all habitat groups, suggesting that they are very versatile and highly adaptable to different types of environment. Rock pools or water pockets with clear water formed on the bank of rivers and waterfalls were the most common habitats associated with An. maculatus. Environmental variables influence the suitability of aquatic habitats for anopheline and culicine larvae, but not significantly associated with the occurrence of both larvae genera (p>0.05). This study provides information on mosquito ecology in relation to breeding habitats that will be useful in designing and implementing larval control operations.
Anopheles cracens has been incriminated as a vector for the simian malaria parasite, Plasmodium knowlesi, that is the fifth Plasmodium species infecting humans. Little experimental data exists on this mosquito species due to the lack of its availability in laboratories.
Common purslane (Portulaca oleracea), also known as pigweed, fatweed, pusle, and little hogweed, is an annual succulent herb in the family Portulacaceae that is found in most corners of the globe. From the ancient ages purslane has been treated as a major weed of vegetables as well as other crops. However, worldwide researchers and nutritionists have studied this plant as a potential vegetable crop for humans as well as animals. Purslane is a nutritious vegetable with high antioxidant properties and recently has been recognized as the richest source of α-linolenic acid, essential omega-3 and 6 fatty acids, ascorbic acid, glutathione, α-tocopherol and β-carotene. The lack of vegetable sources of ω-3 fatty acids has resulted in a growing level of attention to introduce purslane as a new cultivated vegetable. In the rapid-revolutionizing worldwide atmosphere, the ability to produce improved planting material appropriate to diverse and varying rising conditions is a supreme precedence. Though various published reports on morphological, physiological, nutritional and medicinal aspects of purslane are available, research on the genetic improvement of this promising vegetable crop are scant. Now it is necessary to conduct research for the genetic improvement of this plant. Genetic improvement of purslane is also a real scientific challenge. Scientific modernization of conventional breeding with the advent of advance biotechnological and molecular approaches such as tissue culture, protoplast fusion, genetic transformation, somatic hybridization, marker-assisted selection, qualitative trait locus mapping, genomics, informatics and various statistical representation have opened up new opportunities of revising the relationship between genetic diversity, agronomic performance and response to breeding for varietal improvement. This review is an attempt to amalgamate the assorted scientific information on purslane propagation, cultivation, varietal improvement, nutrient analyses, medicinal uses and to describe prospective research especially for genetic improvement of this crop.
We collected data on the trade of seven turtle and tortoise species endemic to Indonesia and Malaysia (Amyda cartilaginea, Batagur borneoensis, Cuora amboinensis, Carettochelys insculpta, Heosemys annandalii, Heosemys grandis, and Heosemys spinosa). The data on those species included: operations costs of three breeding farms and one export facility; species life-history traits; and species international legal trade and confiscation data. We collected data for the facilities (one in Malaysia and three in Indonesia) using site visits and a semi-structured questionnaire. We conducted a literature review to compile relevant information on species' life-history traits to estimate breeding viability. We downloaded species-specific data on international trade from the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) Trade Database for the exporting countries (Malaysia and Indonesia) for 2000-2015. We compared legal trade with confiscation data obtained from CITES. The data in this article can provide insights into the operations of turtle breeding farms in Southeast Asia. These data can be used as a reference for the inspection of breeding farms and for legislative bodies to determine whether captive breeding for select turtle species is feasible.