Increasing world population, shrinking cultivable rice (Oryza sativa L.) land area, water scarcity and excess, evolution of new biotypes of pests and diseases, and climate change pose serious ...challenges to rice breeders to increase production and productivity with multiple resistances to biotic and abiotic stresses. Recent advances in rice genomics research and completion of the rice genome sequence have made it possible to identify and map precisely a number of genes through linkage to DNA markers. Noteworthy examples of some of the genes tightly linked to markers are resistance to or tolerance of blast, bacterial blight, virus diseases, brown planthopper (Nilaparvata lugens), drought, submergence, salinity, and low temperature and improved agronomic and grain quality traits. Marker-assisted selection (MAS) can be used for monitoring the presence or absence of these genes in breeding populations and can be combined with conventional breeding approaches. Marker-assisted backcross breeding has been used to effectively integrate major genes or quantitative trait loci with large effect into widely grown varieties. Pyramiding different resistance genes using MAS provides opportunities to breeders to develop broad-spectrum resistance for diseases and insects. The use of cost-effective DNA markers derived from the fine mapped position of the genes for important agronomic traits and MAS strategies will provide opportunities for breeders to develop high-yielding, stress-resistant, and better-quality rice cultivars.
Submergence stress regularly affects 15 million hectares or more of rainfed lowland rice areas in South and Southeast Asia. A major QTL on chromosome 9, Sub1, has provided the opportunity to apply ...marker assisted backcrossing (MAB) to develop submergence tolerant versions of rice cultivars that are widely grown in the region. In the present study, molecular markers that were tightly linked with Sub1, flanking Sub1, and unlinked to Sub1 were used to apply foreground, recombinant, and background selection, respectively, in backcrosses between a submergence-tolerant donor and the widely grown recurrent parent Swarna. By the BC₂F₂ generation a submergence tolerant plant was identified that possessed Swarna type simple sequence repeat (SSR) alleles on all fragments analyzed except the tip segment of rice chromosome 9 that possessed the Sub1 locus. A BC₃F₂ double recombinant plant was identified that was homozygous for all Swarna type alleles except for an approximately 2.3-3.4 Mb region surrounding the Sub1 locus. The results showed that the mega variety Swarna could be efficiently converted to a submergence tolerant variety in three backcross generations, involving a time of two to three years. Polymorphic markers for foreground and recombinant selection were identified for four other mega varieties to develop a wider range of submergence tolerant varieties to meet the needs of farmers in the flood-prone regions. This approach demonstrates the effective use of marker assisted selection for a major QTL in a molecular breeding program.
Low temperature or cold stress is one of the major constraints of rice production and productivity in temperate rice-growing countries and high-altitude areas in the tropics. Even though low ...temperature affects the rice plant in all stages of growth, the percent seed set is damaged severely by cold and this reduces the yield potential of cultivars significantly. In this study, a new source of cold-tolerant line, IR66160-121-4-4-2, was used as a donor parent with a cold-sensitive cultivar, Geumobyeo, to produce 153 F₈ recombinant inbred lines (RILs) for quantitative trait locus (QTL) analysis. QTL analysis with 175 polymorphic simple sequence repeat (SSR) markers and composite interval mapping identified three main-effect QTLs (qPSST-3, qPSST-7, and qPSST-9) on chromosomes 3, 7, and 9. The SSR markers RM569, RM1377, and RM24545 were linked to the identified QTLs for cold tolerance with respect to percent seed set using cold-water (18-19°C) irrigation in the field and controlled air temperature (17°C) in the greenhouse. The total phenotypic variation for cold tolerance contributed by the three QTLs was 27.4%. RILs with high percent seed set under cold stress were validated with linked DNA markers and by haplotype analysis that revealed the contribution of progenitor genomes from the tropical japonica cultivar Jimbrug (Javanica) and temperate japonica cultivar Shen-Nung89-366. Three QTLs contributed by the cold-tolerant parent were identified which showed additive effect on percent seed set under cold treatment. This study demonstrated the utility of a new phenotyping method as well as the identification of SSR markers associated with QTLs for selection of cold-tolerant genotypes to improve temperate rice production.
Low‐temperature stress is an important factor affecting the growth and development of rice (Oryza sativa L.) in temperate and high‐elevation areas. Cold stress may cause various seedling injuries, ...delayed heading and yield reduction due to spikelet sterility. In this study, 181 microsatellite marker loci were used to identify quantitative trait loci (QTLs) associated with cold tolerance at the vegetative stage in 191 recombinant inbred lines (RILs) derived from a cross of a cold‐tolerant temperate japonica cultivar (M‐202) with a cold‐sensitive indica cultivar (IR50). Different temperature regimes were applied in growth chambers on 191 RILs. The temperature regimes imposed in the growth chamber simulated cold‐stress injuries at the seedling and late vegetative stages. In this study a major QTL was identified on chromosome 12, designated as qCTS12a, that was closely associated with cold‐induced necrosis and wilting tolerance, and accounted for 41% of the phenotypic variation. A number of QTLs with smaller effects were also detected on eight rice chromosomes.
Direct seeding of rice is increasingly being practiced in both rainfed and irrigated areas because of labor shortage for transplanting and opportunities for crop intensification. However, poor crop ...establishment remains a major obstacle facing its large-scale adoption in areas prone to flooding. Screening of over 8,000 gene bank accessions and breeding lines identified a few tolerant genotypes. One of these, Khao Hlan On, was selected for mapping QTLs associated with tolerance using a backcross population with IR64 as a recurrent parent. Survival of BC₂F₂ lines varied from 0 to 68%, and averaged about 28%. A linkage map of 1475.7 cM with an average interval of 11.9 cM was constructed using 135 polymorphic SSRs and 1 indel marker. Five putative QTLs were detected, on chromosomes 1 (qAG-1-2), 3 (qAG-3-1), 7 (qAG-7-2), and 9 (qAG-9-1 and qAG-9-2), explaining 17.9 to 33.5% of the phenotypic variation, and with LOD scores of 5.69-20.34. Khao Hlan On alleles increased tolerance of flooding during germination for all the QTLs. Graphical genotyping of the lines with highest and lowest survival verified the detected QTLs that control tolerance and some QTLs co-localize with previously identified QTLs for traits relevant to tolerance, which warrant further studies.
•Marker-assisted backcross improvement of mega varieties of rice.•QTLs for drought, submergence and salt tolerance.•Foreground and recombinant selection.•Background selection using high density 50K ...SNP chip.
Rice is a staple cereal of India cultivated in about 43.5Mha area but with relatively low average productivity. Abiotic factors like drought, flood and salinity affect rice production adversely in more than 50% of this area. Breeding rice varieties with inbuilt tolerance to these stresses offers an economically viable and sustainable option to improve rice productivity. Availability of high quality reference genome sequence of rice, knowledge of exact position of genes/QTLs governing tolerance to abiotic stresses and availability of DNA markers linked to these traits has opened up opportunities for breeders to transfer the favorable alleles into widely grown rice varieties through marker-assisted backcross breeding (MABB). A large multi-institutional project, “From QTL to variety: marker-assisted breeding of abiotic stress tolerant rice varieties with major QTLs for drought, submergence and salt tolerance” was initiated in 2010 with funding support from Department of Biotechnology, Government of India, in collaboration with International Rice Research Institute, Philippines. The main focus of this project is to improve rice productivity in the fragile ecosystems of eastern, northeastern and southern part of the country, which bear the brunt of one or the other abiotic stresses frequently. Seven consistent QTLs for grain yield under drought, namely, qDTY1.1, qDTY2.1, qDTY2.2, qDTY3.1, qDTY3.2, qDTY9.1 and qDTY12.1 are being transferred into submergence tolerant versions of three high yielding mega rice varieties, Swarna-Sub1, Samba Mahsuri-Sub1 and IR 64-Sub1. To address the problem of complete submergence due to flash floods in the major river basins, the Sub1 gene is being transferred into ten highly popular locally adapted rice varieties namely, ADT 39, ADT 46, Bahadur, HUR 105, MTU 1075, Pooja, Pratikshya, Rajendra Mahsuri, Ranjit, and Sarjoo 52. Further, to address the problem of soil salinity, Saltol, a major QTL for salt tolerance is being transferred into seven popular locally adapted rice varieties, namely, ADT 45, CR 1009, Gayatri, MTU 1010, PR 114, Pusa 44 and Sarjoo 52. Genotypic background selection is being done after BC2F2 stage using an in-house designed 50K SNP chip on a set of twenty lines for each combination, identified with phenotypic similarity in the field to the recipient parent. Near-isogenic lines with more than 90% similarity to the recipient parent are now in advanced generation field trials. These climate smart varieties are expected to improve rice productivity in the adverse ecologies and contribute to the farmer’s livelihood.
Low temperature stress is common for rice grown in temperate regions and at high elevations in the tropics. The most senstive stage to this stress is booting, about 11 days before heading. Japonica ...cultivars are known to be more tolerant than indicas. We constructed a genetic map using 191 recombinant inbred lines derived from a cross between a temperate japonica, M-202, and a tropical indica, IR50, in order to locate quantitative trait loci (QTLs) conferring cold tolerance. The map with a total length of 1,276.8 cM and an average density of one marker every 7.1 cM was developed from 181 loci produced by 175 microsatellite markers. Cold tolerance was measured as the degree of spikelet sterility of treated plants at a 12 degrees C temperature for 5 days in the growth chamber. QTLs on chromosomes 1, 2, 3, 5, 6, 7, 9 and 12 were identified to confer cold tolerance at the booting stage. The QTL contribution to the phenotypic variation ranged from 11 to 17%. The two QTLs with the highest contribution to variation, designated qCTB2a and qCTB3, were derived from the tolerant parent, M-202, each explaining approximately 17% of the phenotypic variance. Two of the eight QTLs for cold tolerance were contributed by IR50.
A novel method for generating plant DNA markers was developed based on data mining for short conserved amino acid sequences in proteins and designing polymerase chain reaction (PCR) primers based on ...the corresponding DNA sequence. This method uses single 15- to 19-mer primers for PCR and an annealing temperature of 50°C. PCR amplicons are resolved using standard agarose gel electrophoresis. Using a reference set of rice genotypes, reproducible polymorphisms were generated. Since primers were designed using highly conserved regions of genes, markers should be generated in other plant species. We propose that this method could be used in conjunction with or as a substitute to other technically simple dominant marker methods for applications such as targeted quantitative trait loci mapping, especially in laboratories with a preference for agarose gel electrophoresis.
Flooding is one of the major hazards of rice production for the rainfed lowland rice ecosystem, and tolerant cultivars are urgently needed to help protect farmers from submergence damage. A quick and ...efficient strategy was implemented to introgress SUB1, a major QTL for submergence tolerance, into a rainfed lowland mega variety BR11 of Bangladesh by only two backcrosses and one selfing generation. In marker-assisted backcrossing (MABC), one tightly-linked simple sequence repeat (SSR) and two gene-based markers, four flanking SSR and 116 background SSR markers were used for foreground, recombinant and background selection, respectively, in backcrosses between a SUB1 donor IR40931-33-1-3-2 and BR11. BR11-Sub1, identified in a BC₂F₂ plant, possessed BR11 type SSR alleles on all fragments analyzed except the SUB1 QTL. The introgression size in BR11-Sub1 was 800 Kb indicating approximately 99.8% identity to BR11. BR11-Sub1 along with other introgression lines showed submergence tolerance similar to the tolerant parent. Yield, yield-component parameters and grain physico-chemical properties showed successful recovery of the BR11 traits in BR11-Sub1, with yield potential ranging from 5.2 to 5.6 t/ha, not significantly different from the recurrent parent mega variety BR11. Producing a large number (~1000) of backcross F₁ plants was considered essential to achieve recombination on both sides of the gene, limiting linkage drag with only two backcrosses. A large number of background markers ensured proper recovery of the recurrent parent genome in the BC₂F₂ generation. The study demonstrates a rapid and highly precise strategy to introgress a major QTL by BC₂F₂ generation into a modern rice variety using an unadapted donor. The variety can replace BR11 on more than 2 million of ha in Bangladesh and provide major increases in rice production.
► Submergence risks and farmers’ preferences should guide breeding for Sub1 rice. ► Socioeconomic and ecological conditions influence preferences for rice cultivars. ► Varying types of flooding ...contribute rice production losses ranging from 10% to 77%. ► Rice varieties with
SUB1 gene survive flooding of two weeks, with varying results. ► Enhancing adoption needs participatory approaches to varietal development.
Rice (
Oryza sativa L.) provides a life support system to millions of resource-poor farmers in rainfed environments; however, yields are very low because of various biotic and abiotic stresses. Submergence caused by typhoons and floods is one of the major reasons for production losses. Because of the complexity of these ecosystems, the breeding framework necessitates adequate feedback and a more in-depth understanding of the ecological and socioeconomic conditions in these flood-prone areas. Within this purview, this study validated the performance in farmers’ fields of lines with the
SUB1 gene that confers tolerance of submergence for up to two weeks. The
SUB1 gene was incorporated through marker-assisted backcrossing, MABC. The evaluation was conducted through participatory approaches to gain understanding of the risks as well as farmers’ preferences for these varieties. A baseline survey of 658 farm households accomplished during 2008, focus group discussions, key informant interviews, and adaptability trials were conducted, with focus on farmers commonly affected by submergence in four Southeast Asian countries: the Philippines, Lao PDR, Indonesia, and Southern Viet Nam. The study further examined farmers’ criteria in evaluating new varieties through the participatory varietal selection (PVS) process. Results showed that varying conditions of submergence can influence farmers’ criteria and preferences for rice cultivars. Depending on the timing of flood with respect to growth stage, shorter duration and shallow flashfloods can result in less than 10% production losses while deeper and stagnant water with two weeks’ duration and >100
cm depth can cause damage ranging from 40% to 77%. Major findings of PVS trials and preference analysis indicated that farmers prefer rice cultivars that are tolerant of submergence, have early to medium maturity relative to their commonly grown varieties, are resistant to pests and diseases, and are resistant to lodging, among other traits. To enhance adoption, male and female farmers should be involved in the evaluation process. The results of this study can contribute to enhancing breeding programs to develop appropriate varieties that reduce production losses, improve income, and ultimately reduce poverty incidence in submergence-prone areas.
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