Natural variation in growth and physiology under salt stress in rice: QTL mapping in a Horkuch × IR29 mapping population at seedling and reproductive stages

AbstractSalinity has a significant negative impact on production of rice. To cope with the increased soil salinity due to climate change, we need to develop salt tolerant rice varieties that can maintain their high yield. Rice landraces indigenous to coastal Bangladesh can be a great resource to study the genetic basis of salt adaptation. In this study, we implemented a QTL analysis framework on a reciprocal mapping population between a salt tolerant landrace Horkuch and a high yieldingrice variety IR29. Our aim was to detect genetic loci that contributes to the salt adaptive responses of the two different developmental stages of rice which are very sensitive to salinity stress. We identified 14 QTL for 9 traits and found that most are unique to the specific developmental stage. In addition, we detected a significant effect of the cytoplasmic genome on the QTL model for some traits such as leaf total potassium and filled grain weight. This underscores the importance of considering cytoplasm-nuclear interaction for breeding programs. Along with this, we identified QTL co-localization for multiple traits that highlights the possible constraint of multiple QTL selection for breeding programs due to different contributions of a donor allele for different traits.HighlightsWe identified genetic loci for the salt tolerance response of two different developmental stages of the rice plant and detected significant contribution of cytoplasm-nuclear genome interaction for a few traits.

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QTL analysis of yield-related traits and their association with functional markers in Brassica napus L.

Australian Journal of Agricultural Research ◽

10.1071/ar06350 ◽

2007 ◽

Vol 58 (8) ◽

pp. 759 ◽

Cited By ~ 26

Author(s):

Yuanyuan Li ◽

Jinxiong Shen ◽

Tonghua Wang ◽

Qingfang Chen ◽

Xingguo Zhang ◽

...

Keyword(s):

Brassica Napus ◽

Agronomic Traits ◽

High Yield ◽

Functional Markers ◽

Multiple Traits ◽

Brassica Napus L ◽

Breeding Programs ◽

F2 Population ◽

Expressed Sequence ◽

Simple Sequence

Yield is one of the most important traits in Brassica napus breeding programs. Quantitative trait loci (QTLs) for yield-related traits based on genetic mapping would help breeders to develop high-yield cultivars. In this study, a genetic linkage map of B. napus, containing 142 sequence-related amplified polymorphism (SRAP) markers, 163 functional markers, 160 simple sequence repeat (SSR) markers, and 117 amplified fragment length polymorphism (AFLP) markers, was constructed in an F2 population of 184 individuals resulting from the cross SI-1300 × Eagle. This map covered 2054.51 cM with an average marker interval of 3.53 cM. Subsequently, QTLs were detected for 12 yield-related traits in Wuhan and Jingmen. In total, 133 QTLs were identified, including 14 consistent ones across the 2 locations. Fifteen of 20 linkage groups (LGs) were found to have QTLs for the 12 traits investigated, and most of the QTLs were clustered, especially on LGs N2 and N7, where similar QTL positions were identified for multiple traits. Eight of 10 QTLs for yield per plant (YP) were also associated with number of seeds per silique (SS), number of siliques per plant (SP), and/or 1000-seed weight (SW). In addition, 45 functional markers involved in 39 expressed sequence tags (ESTs) were linked to the QTLs of 12 traits. The present results may serve as a valuable basis for further molecular dissection of agronomic traits in B. napus, and the markers related to QTLs may offer promising possible makers for marker assisted selection.

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Application of Pedimap — a pedigree visualization tool — to facilitate the decisioning of rice breeding in Sri Lanka

10.1101/2020.01.20.912477 ◽

2020 ◽

Author(s):

P.G.R.G. Rathnayake ◽

S.M. Sahibdeen ◽

U.A.K.S. Udawela ◽

C.K. Weebadde ◽

W.M.W. Weerakoon ◽

...

Keyword(s):

Sri Lanka ◽

Molecular Data ◽

High Yield ◽

Phenotypic Traits ◽

Visualization Tool ◽

Rice Breeding ◽

Rice Varieties ◽

Breeding Programs ◽

Improved Varieties ◽

Genomic Characterization

ABSTRACTThe development of rice cultivars with desirable traits is essential. The decision-making is a crucial step in rice breeding programs. The breeders can make efficient and pragmatic decisions if an organized pedigree visualization platform is available for the material of the rice breeding germplasm. The staple food in Sri Lanka is rice, and there is a great demand for improved varieties with high yield and other promising traits. In the present study, the available data of all the rice varieties released by Rice Research and Development Institute, Sri Lanka, and the related landraces and genotypes were arranged in Pedimap, a pedigree visualization tool. Pedimap can showcase pedigree relationships, phenotypic, and molecular data. The Identity by Descent (IBD) probabilities were calculated using FlexQTL software and included in the Pedimap database. The parentage selection based on the variations of phenotypic traits, selection of marker alleles for molecular breeding, and detection of the founders of genetic effects can be swiftly conducted using Pedimap. However, the power of harnessing the value of Pedimap for making breeding decisions relies on the availability of data for the traits, markers, and genomic sequences. Thus, it is imperative to characterize the breeding germplasms using standard phenomic and genomic characterization procedures before organized into Pedimap. Thereby, the worldwide breeding programs can benefit from each other to produce improved varieties to meet global challenges.

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Combination of traits at two developmental stages under salt stress as a measure of tolerance in a reciprocally crossed rice (Oryza sativa) population

Crop and Pasture Science ◽

10.1071/cp19560 ◽

2020 ◽

Vol 71 (4) ◽

pp. 334 ◽

Cited By ~ 2

Author(s):

Sabrina M. Elias ◽

M. Sazzadur Rahman ◽

Sumaiya F. Khan ◽

Sudip Biswas ◽

Taslima Haque ◽

...

Keyword(s):

Oryza Sativa ◽

Salt Stress ◽

Reciprocal Cross ◽

Developmental Stages ◽

Oryza Sativa L ◽

Principal Component ◽

Maturity Stage ◽

Salt Tolerant ◽

Rice Varieties ◽

Breeding Lines

The rice (Oryza sativa L.) landrace Horkuch from Bangladesh maintains efficient photosynthesis and detoxification under salt stress and was therefore considered to be a useful donor for tolerance traits. Reciprocally crossed bi-parental mapping populations were generated from salt-tolerant Horkuch and high-yielding salt-sensitive variety IR29, in order to identify superior salt-tolerant high-yielding lines as donors. The present study reports on the phenotypic screening data of ~300 F3 segregating populations from the reciprocal cross and their parental lines in seedlings and screening of a subset at maturity stage under gradual salt stress of 12 dS m–1 for seedlings and 8 dS m–1 for mature plants. Correlation, broad-sense heritability and principal component analyses for salt tolerance as well as yield-related traits were conducted in the populations at the two developmental stages. Level of salt injury was found to be correlated with traits such as filled grain weight at maturity stage and biomass-related traits at the seedling stage. This association between yield-related and survival traits helped to identify tolerant and sensitive plants, which were predicative of agronomic performance under salt stress. Moreover, use of the reciprocal-cross population showed how cytoplasmic inheritance of specific traits such as K+ concentrations can affect characteristics of donor plants. Measurement of a large number of traits and analysis of their co-inherited interrelation can therefore help identify the best performing plants under salt stress for effective breeding strategies. The data are being utilised in mapping of quantitative trait loci, and selected progenies are being used as breeding lines for producing durable salt-tolerant, high-yielding rice varieties.

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Towards Developing Salinity Tolerant Rice Adaptable for Coastal Regions in Indonesia

KnE Life Sciences ◽

10.18502/kls.v2i6.1021 ◽

2017 ◽

Vol 2 (6) ◽

pp. 72 ◽

Cited By ~ 5

Author(s):

Aris Hairmansis ◽

Nafisah Nafisah ◽

Ali Jamil

Keyword(s):

Salinity Tolerance ◽

Sea Water ◽

Rice Production ◽

Lowland Rice ◽

Rice Breeding ◽

Salt Tolerant ◽

Coastal Regions ◽

Rice Varieties ◽

Breeding Programs ◽

The Impact

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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Collection, conservation, exploitation and development of rice genetic resource of Vietnam

Journal of Vietnamese Environment ◽

10.13141/jve.vol6.no3.pp239-243 ◽

2014 ◽

Vol 6 (3) ◽

pp. 239-243

Author(s):

Duc Bach Nguyen ◽

Van Hai Tong ◽

Van Hung Nguyen ◽

Huu Ton Phan

Keyword(s):

Genetic Resources ◽

Genetic Resource ◽

Economic Benefits ◽

High Yield ◽

Viet Nam ◽

Rice Varieties ◽

Breeding Programs ◽

Rice Germplasm ◽

The North ◽

High Level

Genetic resources are important for the development of every country and for humanity. Collection, conservation and reasonable utilization of genetic resource is required mission. Understanding the importance of genetic resource, especially rice germplasm, since 2001, Center for conservation and development of crop genetic resources (CCD-CGR) of Hanoi University of Agriculture (Vietnam National University of Agriculture) has been collected, conserved and evaluated rice germplasm from different provinces of Vietnam for breeding programs. So far, 1090 accessions of local rice of Vietnam have been collected. Evaluation of agronomic properties and screening of some important genes using DNA molecular markers have revealed that Vietnamese rice germplasm has high level diversity and containing important genes for quality and resistance for disease and pests. These genetic resources are potential materials for national breeding programs. Based on the collected germplasm, 3 new glutinous rice varieties have been successfully created with high yield and good quality. In addition, the degradation of local rice varieties is also a matter of concern. So far, 4 specialty rice varieties Deo Dang, Ble chau, Pu de and Khau dao have been successfully restored for the north provinces of Vietnam. The main results of this study are germplasms for rice breeding programs and new improved varieties that bring economic benefits to farmers and the country. Nguồn gene là tài nguyên sống còn của mỗi quốc gia và của toàn nhân loại. Vì vậy thu thập, bảo tồn, đánh giá và khai thác hợp lý nguồn tài nguyên này có ý nghĩa rất lớn. Nhận thức được tầm quan trọng của nguồn gen nhất là nguồn gen cây lúa, ngay từ đầu những năm 2000, Trung tâm bảo tồn và phát triển nguồn gene cây trồng thuộc Trường Đại học nông nghiệp, nay là Học Viện nông nghiệp Việt Nam đã tiến hành thu thập, lưu giữ, đánh giá và khai thác nguồn gene lúa. Kết quả đã thu thập, lưu giữ được 1090 mẫu giống lúa địa phương Việt Nam. Đánh giá đặc điểm nông sinh học và phát hiện một số gene quy định các tính trạng chất lượng và kháng sâu bệnh bằng chỉ thị phân tử DNA. Đây là nguồn gene quan trọng cho chọn tạo giống. Dựa vào nguồn gene thu thập được, cho đến nay, Trung tâm bảo tồn và phát triển nguồn gene cây trồng đã lai và chọn tạo được thành công 03 giống lúa nếp chất lượng cao. Ngoài ra, thoái hóa giống cũng là vấn đề đang được quan tâm. Cho đến nay 4 giống lúa đặc sản Đèo đàng, Ble châu, Pu đe và Khẩu dao đã được phục tráng và đưa vào sản xuất. Kết quả của những nghiên cứu này là ngân hàng các giống lúa làm nguồn gene để chọn tạo giống mới đem lại lợi ích kinh tế cho người nông dân và đất nước.

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Identification of the Optimum Environments for the High Yield and Quality Traits of Lentil Genotypes Evaluated in Multi-Location Trials

Sustainability ◽

10.3390/su13158247 ◽

2021 ◽

Vol 13 (15) ◽

pp. 8247

Author(s):

Dimitrios N. Vlachostergios ◽

Christos Noulas ◽

Anastasia Kargiotidou ◽

Dimitrios Baxevanos ◽

Evangelia Tigka ◽

...

Keyword(s):

Crude Protein ◽

Agronomic Traits ◽

High Yield ◽

Breeding Programs ◽

Growing Seasons ◽

Yield And Quality ◽

Food And Feed ◽

Superior Genotypes ◽

Selection Of ◽

The Ideal

Lentil is a versatile and profitable pulse crop with high nutritional food and feed values. The objectives of the study were to determine suitable locations for high yield and quality in terms of production and/or breeding, and to identify promising genotypes. For this reason, five lentil genotypes were evaluated in a multi-location network consisting of ten diverse sites for two consecutive growing seasons, for seed yield (SY), other agronomic traits, crude protein (CP), cooking time (CT) and crude protein yield (CPY). A significant diversification and specialization of the locations was identified with regards to SY, CP, CT and CPY. Different locations showed optimal values for each trait. Locations E4 and E3, followed by E10, were “ideal” for SY; locations E1, E3 and E7 were ideal for high CP; and the “ideal” locations for CT were E3 and E5, followed by E2. Therefore, the scope of the cultivation determined the optimum locations for lentil cultivation. The GGE-biplot analysis revealed different discriminating abilities and representativeness among the locations for the identification of the most productive and stable genotypes. Location E3 (Orestiada, Region of Thrace) was recognized as being optimal for lentil breeding, as it was the “ideal” or close to “ideal” for the selection of superior genotypes for SY, CP, CT and CPY. Adaptable genotypes (cv. Dimitra, Samos) showed a high SY along with excellent values for CP, CT and CPY, and are suggested either for cultivation in many regions or to be exploited in breeding programs.

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QTL Mapping of Seedling and Adult Plant Resistance to Septoria Tritici Blotch in Winter Wheat cv. Mandub (Triticum aestivum L.)

Agronomy ◽

10.3390/agronomy11061108 ◽

2021 ◽

Vol 11 (6) ◽

pp. 1108

Author(s):

Dominika Piaskowska ◽

Urszula Piechota ◽

Magdalena Radecka-Janusik ◽

Paweł Czembor

Keyword(s):

Mapping Population ◽

Triticum Aestivum L ◽

Seedling Stage ◽

Septoria Tritici Blotch ◽

Septoria Tritici ◽

Adult Plant ◽

Resistance Locus ◽

Phenotypic Variance ◽

Breeding Programs ◽

Plant Stage

Septoria tritici blotch (STB) is one of the most devastating foliar diseases of wheat worldwide. Host resistance is the most economical and safest method of controlling the disease, and information on resistance loci is crucial for effective breeding for resistance programs. In this study we used a mapping population consisting of 126 doubled-haploid lines developed from a cross between the resistant cultivar Mandub and the susceptible cultivar Begra. Three monopycnidiospore isolates of Z. tritici with diverse pathogenicity were used to test the mapping population and parents’ STB resistance at the seedling stage (under a controlled environment) and adult plant stage (polytunnel). For both types of environments, the percentage leaf area covered by necrosis (NEC) and pycnidia (PYC) was determined. A linkage map comprising 5899 DArTSNP and silicoDArT markers was used for the quantitative trait loci (QTL) analysis. The analysis showed five resistance loci on chromosomes 1B, 2B and 5B, four of which were derived from cv. Mandub. The location of QTL detected in our study on chromosomes 1B and 5B may suggest a possible identity or close linkage with Stb2/Stb11/StbWW and Stb1 loci, respectively. QStb.ihar-2B.4 and QStb.ihar-2B.5 detected on chromosome 2B do not co-localize with any known Stb genes. QStb.ihar-2B.4 seems to be a new resistance locus with a moderate effect (explaining 29.3% of NEC and 31.4% of PYC), conferring resistance at the seedling stage. The phenotypic variance explained by QTL detected in cv. Mandub ranged from 11.9% to 70.0%, thus proving that it is a good STB resistance source and can potentially be utilized in breeding programs.

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Breeding of High Cooking and Eating Quality in Rice by Marker-Assisted Backcrossing (MABc) Using KASP Markers

Plants ◽

10.3390/plants10040804 ◽

2021 ◽

Vol 10 (4) ◽

pp. 804

Author(s):

Me-Sun Kim ◽

Ju-Young Yang ◽

Ju-Kyung Yu ◽

Yi Lee ◽

Yong-Jin Park ◽

...

Keyword(s):

Genetic Background ◽

Amylose Content ◽

Yield Potential ◽

Eating Quality ◽

Breeding Cycle ◽

Recurrent Parent ◽

Rice Varieties ◽

Breeding Programs ◽

Genome Wide ◽

Cooking And Eating Quality

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.

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Improved Rice Technology Adoption: The Role of Spatially-Dependent Risk Preference

Agriculture ◽

10.3390/agriculture11080691 ◽

2021 ◽

Vol 11 (8) ◽

pp. 691

Author(s):

Omotuyole Isiaka Ambali ◽

Francisco Jose Areal ◽

Nikolaos Georgantzis

Keyword(s):

Field Experiments ◽

Climatic Factors ◽

Risk Preferences ◽

Risk Preference ◽

Probit Model ◽

Climatic Conditions ◽

High Yield ◽

Risk Attitudes ◽

Policy Action ◽

Rice Varieties

This study analyses farmers’ adoption of improved rice technology, taking into account farmers’ risk preferences; the unobserved spatial heterogeneity associated with farmers’ risk preferences; farmers’ household and farm characteristics; farm locations, farmers’ access to information, and their perceptions on the rice improved varieties (i.e., high yield varieties, HYV). The study used data obtained from field experiments and a survey conducted in 2016 in Nigeria. An instrumental-variable probit model was estimated to account for potential endogenous farmers’ risk preference in the adoption decision model. Results show that risk averse (risk avoidant) farmers are less likely to adopt HYV, with the spatial lags of farmers’ risk attitudes found to be a good instrument for spatially unobserved variables (e.g., environmental and climatic factors). We conclude that studies supporting policy action aiming at the diffusion of improved rice varieties need to collect information, if possible, on farmers’ risk attitudes, local environmental and climatic conditions (e.g., climatic, topographic, soil quality, pest incidence) in order to ease the design and evaluation of policy actions on the adoption of improved agricultural technology.

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