scholarly journals Utilization of Molecular Markers for Rice Breeding

2021 ◽  
Vol 17 (1) ◽  
pp. 45
Author(s):  
Tasliah Tasliah

Rice is the staple food for more than half of the world's population. Rice production in 2050 must increase by at least 50% to keep up with the population growth. Efforts to increase rice production continue using various strategies. Breeders apply multiple approaches including application of molecular markers in developing varieties better than the previous ones. Since the discovery of the restriction fragment length polymorphism (RFLP) markers in 1980s and the development of polymerase chain reaction (PCR) method, many types of molecular markers have been developed and applied to various crops including rice. Various molecular approaches to map genetic loci associated with rice superior traits were conducted. The mapped loci are very useful for rice breeding purposes. This paper reports the results of mapping and breeding economically important traits in rice, mainly those related to abiotic stresses, agronomic traits, yield, and yield quality. These included characters of semidwarf stature, aromatic grain, high yield potential, eating quality, higher Zn and Fe grain, more tolerant to abiotic stresses, such as salinity, drought, phosphate deficiency, Al toxicity and Fe toxicity, submergence, as well as early maturity character. The mapped characters can be transferred using marker-assisted backcrossing (MABC) method into cultivated rice genotypes well-adopted by farmers. Several countries including Indonesia have benefited from this breeding method, and Indonesia have released several rice varieties developed through MABC. These include rice varieties such as Code, Angke, Inpari 30, Inpari Blas, Inpari HDB, Bio Patenggang Agritan, and Bioni 63 Ciherang Agritan

2018 ◽  
Vol 55 (1) ◽  
pp. 143-156
Author(s):  
M. MOGGA ◽  
J. SIBIYA ◽  
H. SHIMELIS ◽  
J. LAMO ◽  
N. OCHANDA

SUMMARYRice (Oryza sativa L.) is an important staple crop in South Sudan. Current rice consumption in the country is approximately 23,000 mg year−1 of which more than 75% is imported. We investigated farmers’ perceived rice production and productivity constraints and choice of rice ideotypes across rainfed and irrigated rice agro-ecologies in South Sudan to guide breeding and policy interventions. Data were gathered through participatory rural approaches and a formal structured survey involving 136 rice farmers from major rice growing areas of South Sudan. Farmers generally cultivated old rice varieties with low yields varying from 0.4 to 1.6 mg ha−1. Pair-wise ranking based on respondents score indicated yield, early maturity, cooking and eating quality, nutritional importance and drought tolerance as the most desirable traits of rice ideotypes. Further, imported rice varieties were best ranked for their sweet and appealing taste, rich aroma, grain shape and size, swelling capacity and non-stickiness during cooking. Major perceived constraints to rice production were unreliable rainfall, poor access to credit facilities, poor soil and water management practices, poor rice storage facilities, inadequate and poor processing machines as well as limited technical skills in rice production. The results show a need for integration of farmers’ and stakeholders’ preferences in variety development process and the desirability of releasing site-specific rice cultivars given the differences in bio-physical, socio-cultural and farmers preferences across major rice growing areas of South Sudan.


Plants ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 804
Author(s):  
Me-Sun Kim ◽  
Ju-Young Yang ◽  
Ju-Kyung Yu ◽  
Yi Lee ◽  
Yong-Jin Park ◽  
...  

The primary goals of rice breeding programs are grain quality and yield potential improvement. With the high demand for rice varieties of premium cooking and eating quality, we developed low-amylose content breeding lines crossed with Samgwang and Milkyqueen through the marker-assisted backcross (MABc) breeding program. Trait markers of the SSIIIa gene referring to low-amylose content were identified through an SNP mapping activity, and the markers were applied to select favorable lines for a foreground selection. To rapidly recover the genetic background of Samgwang (recurrent parent genome, RPG), 386 genome-wide markers were used to select BC1F1 and BC2F1 individuals. Seven BC2F1 lines with targeted traits were selected, and the genetic background recovery range varied within 97.4–99.1% of RPG. The amylose content of the selected BC2F2 grains ranged from 12.4–16.8%. We demonstrated the MABc using a trait and genome-wide markers, allowing us to efficiently select lines of a target trait and reduce the breeding cycle effectively. In addition, the BC2F2 lines confirmed by molecular markers in this study can be utilized as parental lines for subsequent breeding programs of high-quality rice for cooking and eating.


2020 ◽  
Author(s):  
Nitika Sandhu ◽  
Shailesh Yadav ◽  
Arvind Kumar

Increasing incidences of multiple abiotic stresses together with increasing population are the major constraints to attain the global food security. Rice, the major staple food crop is very much prone to various abiotic and biotic stresses, which can occur one at a time or two or more together in a single crop growing season and adversely affects the rice production and productivity. The devastating effect of multiple stresses on rice crop is much more erratic and complex leading to higher losses in the crop grain yield. The concurrent occurrence of multiple streeses can destroy rice production in many of the rainfed areas of South and Southeast-Asia. Genomics-assisted breeding strategies have been instrumental in introgression of various major effect QTLs/genes into rice mega varieties and have proven successful in achieving the desired level of tolerance/resistance to various abiotic stresses in diffferent crop species. Keeping the present scenario of changing climate in mind, the chapter discusses the recent past success in combining tolerance to two or more abiotic stresses in mega rice varieties applying genomics-assisted breeding and development of high-yielding climate resilient rice through stacking of multiple genes/QTLs, which can withstand in a cascade of multiple stresses occurring regularly in rainfed environments.


2020 ◽  
Vol 39 (1) ◽  
pp. 11
Author(s):  
Fatimah Fatimah ◽  
Joko Prasetiyono

<p>Bacterial leaf blight (BLB) caused by Xanthomonas oryzae pv oryzae (Xoo) is an important bacterial disease and very destructive to rice plant. BLB decreased rice production from 20%-30% up to 80%. Host-plant resistance is a cost-effective and environmentally safe approach to reduce yield loss. However the development of new rice variety by conventional selection would take several years. The genetic improvement in rice production considered as a vital program in order to ensure national food security. The availability of corresponding molecular marker makes it more precision and efficient by reducing the time required for selection. This present article highlights the molecular approach in breeding for BLB disease resistant rice varieties. In detail, it will be discussed the application of molecular marker assisted backcrossing and pyramiding gene resistance offered breeders to accelerate the rice breeding program for resistance to BLB. The pyramiding of three resistance BLB genes (xa5, Xa7, and Xa21and one gene (Xa4) as a background into two elite indica rice varieties, Ciherang and Inpari 13, was introduced successfully. The combining of conventional breeding, marker assisted backcrossing, disease evaluation, agronomic performance and yield has led the significant resistance of pyramid lines to Xoo Race III, IV and VIII in vegetative and generative phase while their yield potential was maintained (6-7 ton/ha). The current status of Ciherang-HDB and Inpari 13-HDB pyramid lines is the production of nucleoseeds and breeder seeds. This broad spectrum and durable resistance characteristic may help in controlling BLB disease in different region of Indonesia and it will facilitate the rice self-sustainability program.</p><p>Keywords: Rice, gene pyramiding, plant breeding, molecular marker.</p><p> </p><p><strong>Abstrak</strong></p><p>Penyakit hawar daun bakteri (HDB) yang disebabkan oleh Xanthomonas oryzae pv oryzae (Xoo) merupakan penyakit penting pada tanaman padi karena dapat menurunkan produksi padi rata-rata 20-30% bahkan dapat mencapai 80%. Penggunaan varietas tahan merupakan cara pengendalian yang paling efektif, ramah lingkungan, dan mudah dilakukan. Namun pengembangan varietas unggul baru melalui seleksi konvensional memerlukan waktu lebih lama. Perbaikan varietas padi perlu terus dikembangkan dalam mendukung ketahanan pangan dan kemandirian pangan nasional. Tersedianya marka molekuler membantu proses pemuliaan tanaman menjadi lebih presisi dan lebih efisien sehingga mengurangi waktu seleksi pada tanaman progeni. Tulisan ini memfokuskan pendekatan molekuler dalam pemuliaan varietas tahan penyakit HDB melalui piramida gen ketahanan untuk mempercepat progam pemuliaan padi tahan penyakit HDB. Kegiatan menggabungkan tiga gen ketahanan (xa5, Xa7, dan Xa21) dan satu gen (Xa4) sebagai background ke dalam padi varietas Ciherang dan Inpari-13 telah berhasil dilakukan. Melalui penggabungan beberapa pendekatan yaitu pemuliaan konvensional dan silang balik berbantu marka, evaluasi penyakit dan keragaan agronomi serta komponen hasil telah menunjukkan peningkatan ketahanan yang nyata pada galur-galur piramida Ciherang HDB dan Inpari-13 HDB pada tiga ras Xoo (Ras III, IV, dan VIII), baik pada fase vegetatif maupun generatif dengan potensi hasil tidak berbeda nyata dengan tetuanya (6-7 t/ha). Saat ini sudah diproduksi benih inti (NS) dan benih penjenis (BS) galur-galur piramida Ciherang HDB dan Inpari-13 HDB. Dengan demikian, galur-galur piramida memiliki spektrum yang luas dan mampu bertahan dalam jangka waktu lama sehingga dapat mengontrol penyakit HDB di berbagai wilayah Indonesia dan mendukung target pemerintah untuk mempertahankan swasembada beras secara berkelanjutan.</p><p>Kata kunci: Padi, piramida gen, pemuliaan tanaman, marka molekuler.<br /><br /></p><p> </p>


Author(s):  
Engku Hasmah Engku Abdullah ◽  
Azizah Misran ◽  
Muhammad Nazmin Yaapar ◽  
Mohd Rafii Yusop ◽  
Asfaliza Ramli

Silicon (Si) is a micronutrient that can increase the resistance of certain plants against multiple biotic or abiotic stresses. It is known that Si has a beneficial effect on plant growth, beginning in the soil, which could lead to a good crop yield. Despite its benefits, Si is not listed among the generally essential elements or nutrients for rice production in many countries such as Malaysia. This review discusses the ability to uptake Si and its benefits on rice. Environmental factors affect rice production, and among the factors, high temperature has been shown to disrupt the physiological development of rice grain, which contributes to chalkiness. Chalkiness is an undesirable trait that decreases grain’s value, milling, cooking, and eating quality. The application of Si could ameliorate rice grain quality, thus providing a valuable reference for Si fertiliser use in high-quality rice production. This review also presents an update on the potentials of Si in improving the rice yield and grain quality, including Si’s ability to minimise grain chalkiness. Therefore, it is anticipated that Si applications will increase rice yield and grain quality and help to reduce chalkiness.


1970 ◽  
Vol 11 ◽  
pp. 57-62 ◽  
Author(s):  
Sudha Sapkota ◽  
Mina Nath Paudel ◽  
Naresh Singh Thakur ◽  
Megh Bahadur Nepali ◽  
Reshma Neupane

Rice (Oryza sativa L.) is a staple crop of Nepal and is directly associated with ample water and minimum fluctuation of temperature that could affect on its production. Jumla is the unique place where rice is cultivated in the highest altitude (3000 m) in the world. To find out changes in rice production due to climatic effect, six VDCs of Jumla were chosen for the study. Household survey, participatory rapid appraisal, farmers’ group discussions and desk review were used for collecting data. Rice varieties Chandannath-1 andChandannath-3 were disseminated by the formal seed system with the aim of increasing rice productivity. Despite the replacement of local varieties by improved ones the production trend seems to be stagnant. One of the factors on stagnant of rice production in Jumla is due to the lack of desirable variety with genetic traits of early maturity, less nutrient requirement compared to Jumli Marshi to cope up with the climate congruently supporting to cultural practices regarding the unique rice production systems of Jumla. Key words: climate change; rice production; highest altitude; seed DOI: 10.3126/njst.v11i0.4124Nepal Journal of Science and Technology 11 (2010) 57-62


2021 ◽  
Vol 13 (4) ◽  
pp. 2078
Author(s):  
Manzoor H. Dar ◽  
Dilruba A. Bano ◽  
Showkat A. Waza ◽  
Najam W. Zaidi ◽  
Asma Majid ◽  
...  

Rice is globally a major food crop and its production has progressively been affected by various types of abiotic stresses especially drought, flooding, salinity, heat and cold in most of the cultivable rice ecosystems. The incidence, intensity and duration of these stresses are anticipated to aggravate due to climate change consequences, demanding resilient yields in these situations to be essential. Present paper deals with reviewing various types of abiotic stresses and their mitigation strategies for enhancing and stabilizing rice production in stress prone areas. Review of available literature pertaining to the study area has been used as research methodology for this paper. The available literature suggests that stress-tolerant varieties can serve as the most viable strategy to contribute in coping with the problem of abiotic stresses. Although, good progress has been made in the development of stress-tolerant rice varieties (STRVs) and incessant efforts are being made to spread these varieties in target areas, adoption by farmers is yet to meet expectations. Advantage, affordability, awareness and availability are the main factors responsible for adopting of any technology. The adoption of stress-tolerant varieties has not reached its potential, predominantly due to the lack of awareness and non-availability of seeds amongst farmers. Strategic and intentional collaborations should be ensured for scaling the sustainable delivery and diffusion of STRVs. A promotional roadmap that ensures the linkages between private and public seed sectors remains the key factor for its successful adoption. Similarly, strengthening of formal, informal and semi-formal seed systems is crucial to accelerate the dissemination of these varieties. There is an imperative need to create strategic plans for the development of varieties possessing multiple stress tolerance. Significant investments for sustainability of rice production in stress prone areas form the essential component of long-term agricultural development. The sooner these investments and strategies are accomplished, the greater the gains are expected.


Author(s):  
Budi Winarto ◽  
Sodiq Jauhari

<p><strong>Morphology Performances and Yield of New Superior</strong><strong> Rice Variety with Integrated Crop Management in Rainfedland Jepara District</strong>. One constraint for increasing rice production in rainfedland Jepara District is the availability of adaptive improved rice varieties with high yield. The purpose of this assessment are: (1) to analyze the morphological performance and yield potential of some new superior varieties in rainfedland Jepara District (2) to assess the level of main rice pest and diseases attack and the presence of natural pest’s enemies, and (3) to assess the responses and perceptions of farmers towards integrated crop management applications in rice production. The assessment was conducted in ranfedland Mayong Kidul Village, Mayong Sub-district, Jepara District by involving Lestari Farmer’s Group on the second planting season of 2015. The assessment also employed A Randomized Block Design with three replications and rice variety as treament: Inpari-30, Inpari-31, Inpari-10, Conde, mekongga and varietas Ciherang as the control variety.  The collected data of morphology and rice yield were analyzed using analysis of variance,  then the mean difference values between treatments was further tested using the least significant difference test at p = 0.05. The results showed that there were influences of rice varieties on plant height, number of tillers, pests and diseaces as well as yield and yield component of the five rice varieties. The Mekongga variety is the most suitable rice variety that could be used in rainfedland in order to improve rice productivity in rainfedland of Jepara District. This variety could produce dry rice grain up to 6.8 tons/ha, with 105.5 cm plant height, 14.1 productive tillers, 23.7 cm panicle length 566 and 176 number of filled and empty grains 5 panicles respectively, 4.5 pest and diceases attack level, and is able to increase grain yield up to 30.7% compared to that of control variety. Respondent farmers have a positive perception to the concept of integrated crop management with a value of 68.3%. The implication of these results is that the utilization of new superior rice varieties especially Mekongga have a high potential for improving rice productivity in rainfedland of Jepara District. <em></em></p><p> <strong>Keywords</strong>: <em>New Superior Rice Varieties,</em><em> rainfedland, ICM, Jepara</em></p><p align="center"><strong> </strong></p><p align="center"><strong>ABSTRAK</strong></p><p align="center"><strong> </strong></p><p>Keragaan Morfologi dan Hasil Varietas Unggul Baru Padi dengan Pengelolaan Tanaman Terpadu di Kabupaten Jepara.  Salah satu kendala peningkatan produktivitas padi di lahan sawah tadah hujan Kabupaten Jepara adalah ketersediaan varietas unggul yang adaptif dengan produktivitas tinggi. Tujuan pengkajian ini adalah (1) mengkaji keragaan morfologi dan potensi hasil beberapa VUB padi di lahan sawah tadah hujan (2) mengkaji tingkat serangan hama dan penyakit utama padi serta keberadaan musuh alami hama, dan (3) mengkaji respon dan persepsi petani terhadap penerapan PTT padi. Pengkajian dilakukan di lahan sawah tadah hujan Desa Mayong Kidul Kecamatan Mayong Kabupaten Jepara, Kelompok Tani Lestari pada musim tanam ke-2 tahun 2015<em>. </em>Pengkajian ini menggunakan Rancangan Acak Kelompok dengan tiga ulangan dan sebagai perlakuan adalah varietas padi: Inpari-30, Inpari-31, Inpari-10, Conde dan mekongga serta varietas Ciherang sebagai pembanding. Data yang terkumpul dianalisis menggunakan analisis varian (anova), selanjutnya perbedaan nilai tengah antar perlakuan diuji lanjut menggunakan uji beda nyata terkecil (BNT) pada p=0.05. Hasil pengkajian menunjukkan bahwa terdapat pengaruh nyata varietas padi terhadap tinggi tanaman, jumlah anakan, perkembangan OPT, hasil dan komponen hasil gabah dari kelima varietas tanaman padi yang diuji. Varietas Mekongga merupakan VUB padi yang paling sesuai ditanam di lokasi pengkajian dalam rangka meningkatkan produktivitas padi. Varietas ini menghasilkan gabah kering giling hingga 6.8 ton/ha, tinggi tanaman 105.5 cm, jumlah anakan produktif 14.1, panjang malai  23.7 cm, jumlah gabah bernas 566 butir  per 5 malai, jumlah gabah hampa 176 gabah hampa per 5 malai dan tingkat serangan OPT 4,5%, serta  mampu meningkatkan hasil gabah hingga 30.7% dibanding kontrol. Petani juga memiliki persepsi positif terhadap konsep PTT dengan nilai mencapai 68.3%. Implikasi hasil kajian ini adalah pemanfaatan VUB padi terutama Mekongga memiliki potensi tinggi dalam meningkatkan produktivitas padi di lahan sawah tadah hujan Kabupaten Jepara.</p><p><strong> </strong><strong>Kata kunci</strong>: <em>VUB padi, tadah hujan, PTT, Jepara</em></p><p> </p>


Author(s):  
Roel Rabara ◽  
Joseph Msanne ◽  
Marilyn Ferrer ◽  
Supratim Basu

Rice production, owing to its high-water requirement for cultivation, is very vulnerable to the threat of changing climate, particularly prolonged drought and high temperature. Such threats heighten the need for abiotic stress-resilient rice varieties with better yield potential. This review examines the physiological and molecular mechanisms of rice varieties to cope with stress conditions of drought (DS), high temperature (HTS) and their combination (DS-HTS). It appraises research studies in rice about its various phenotypic traits, genetic loci and response mechanisms to stress conditions to help craft new breeding strategies for rice varieties with improved resilience to abiotic stresses. This review consolidates available information on promising rice cultivars with desirable traits as well as advocates synergistic and complementary approaches in molecular and systems biology to develop new rice breeds that favorably respond to climate-induced abiotic stresses. The development of new breeding and cultivation strategies for climate-resilient rice varieties is a challenging task. It requires a comprehensive understanding of the various morphological, biochemical, physiological, and molecular components governing yield under drought and high temperature, but possible by implementing cohesive approaches involving molecular and systems biology approaches in genomics and molecular breeding, including genetic engineering.


2017 ◽  
Vol 2 (6) ◽  
pp. 72 ◽  
Author(s):  
Aris Hairmansis ◽  
Nafisah Nafisah ◽  
Ali Jamil

Lowland rice areas along the coastal regions are a major contributor for rice production in Indonesia. Sustainability of rice production in those areas is challenged by the increase of soil salinity as the result of sea water inundation. The problem is exacerbated by the increase of sea water level as the impact of global climate change. High concentration of salt ion in the soil could significantly reduce rice growth and yield. Development of salinity tolerant rice varieties is therefore important to maintain sustainability of rice production in the coastal regions. Breeding programs to improve salinity tolerance of Indonesian rice has been established in Indonesian Centre for Rice Research. Through intensive salt tolerant screening program genetic variations in salinity tolerance have been identified within rice germplasm allowing the improvement of salinity tolerant of existing rice varieties. Different genetic resources have been used for salinity tolerant improvement including landraces, improved varieties and introduction lines. A number of promising salt tolerant rice breeding lines have been developed and showed adaptability to salt affected areas in the lowland coastal areas. Two new salt tolerant rice varieties have been released recently which are adaptable to salt affected areas. This paper will describe the progress in the breeding programs to develop salt tolerant rice for lowland rice areas in the coastal regions. Strategy to accelerate the improvement of the salinity tolerant of Indonesian rice varieties in the future will be also discussed.Keywords: rice, breeding, salinity tolerance, coastal regions.


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