scholarly journals Meta-QTL and ortho-MQTL analyses identified genomic regions controlling rice yield, yield-related traits and root architecture under water deficit conditions

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Bahman Khahani ◽  
Elahe Tavakol ◽  
Vahid Shariati ◽  
Laura Rossini
Keyword(s):  
Water Deficit ◽  
Root Architecture ◽  
Agronomic Traits ◽  
Heading Date ◽  
Dry Weight ◽  
Genetic Dissection ◽  
Rice Varieties ◽  
Average Confidence ◽  
Stable Qtls ◽  
Genomic Regions

AbstractMeta-QTL (MQTL) analysis is a robust approach for genetic dissection of complex quantitative traits. Rice varieties adapted to non-flooded cultivation are highly desirable in breeding programs due to the water deficit global problem. In order to identify stable QTLs for major agronomic traits under water deficit conditions, we performed a comprehensive MQTL analysis on 563 QTLs from 67 rice populations published from 2001 to 2019. Yield and yield-related traits including grain weight, heading date, plant height, tiller number as well as root architecture-related traits including root dry weight, root length, root number, root thickness, the ratio of deep rooting and plant water content under water deficit condition were investigated. A total of 61 stable MQTLs over different genetic backgrounds and environments were identified. The average confidence interval of MQTLs was considerably refined compared to the initial QTLs, resulted in the identification of some well-known functionally characterized genes and several putative novel CGs for investigated traits. Ortho-MQTL mining based on genomic collinearity between rice and maize allowed identification of five ortho-MQTLs between these two cereals. The results can help breeders to improve yield under water deficit conditions.

scholarly journals Genetic Dissection of Grain Yield and Agronomic Traits in Maize under Optimum and Low-Nitrogen Stressed Environments

2020 ◽  
Vol 21 (2) ◽  
pp. 543 ◽  
Author(s):  
Berhanu Tadesse Ertiro ◽  
Michael Olsen ◽  
Biswanath Das ◽  
Manje Gowda ◽  
Maryke Labuschagne
Keyword(s):  
Grain Yield ◽  
Agronomic Traits ◽  
Genotyping By Sequencing ◽  
Genetic Dissection ◽  
Common Qtl ◽  
Chromosome Position ◽  
Maize Varieties ◽  
Dh Lines ◽  
Genomic Regions ◽  
Low Nitrogen

Understanding the genetic basis of maize grain yield and other traits under low-nitrogen (N) stressed environments could improve selection efficiency. In this study, five doubled haploid (DH) populations were evaluated under optimum and N-stressed conditions, during the main rainy season and off-season in Kenya and Rwanda, from 2014 to 2015. Identifying the genomic regions associated with grain yield (GY), anthesis date (AD), anthesis-silking interval (ASI), plant height (PH), ear height (EH), ear position (EPO), and leaf senescence (SEN) under optimum and N-stressed environments could facilitate the use of marker-assisted selection to develop N-use-efficient maize varieties. DH lines were genotyped with genotyping by sequencing. A total of 13, 43, 13, 25, 30, 21, and 10 QTL were identified for GY, AD ASI, PH, EH, EPO, and SEN, respectively. For GY, PH, EH, and SEN, the highest number of QTL was found under low-N environments. No common QTL between optimum and low-N stressed conditions were identified for GY and ASI. For secondary traits, there were some common QTL for optimum and low-N conditions. Most QTL conferring tolerance to N stress was on a different chromosome position under optimum conditions.

scholarly journals Evidence of selection, adaptation and untapped diversity in Vietnamese rice landraces

2020 ◽  
Author(s):  
Janet Higgins ◽  
Bruno Santos ◽  
Tran Dang Khanh ◽  
Khuat Huu Trung ◽  
Tran Duy Duong ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Heading Date ◽  
Cultivated Rice ◽  
Region Of Origin ◽  
Rice Varieties ◽  
Rice Landraces ◽  
Shared Ancestry ◽  
Production Areas ◽  
Genomic Regions ◽  
New Generation

AbstractVietnam possesses a vast diversity of rice landraces due to its geographical situation, latitudinal range, and a variety of ecosystems. This genetic diversity constitutes a highly valuable resource at a time when the highest rice production areas in the low-lying Mekong and Red River Deltas are enduring increasing threats from climate changes, particularly in rainfall and temperature patterns.We analysed 672 Vietnamese rice genomes, 616 newly sequenced, that encompass the range of rice varieties grown in the diverse ecosystems found throughout Vietnam. We described four Japonica and five Indica subpopulations within Vietnam likely adapted to the region of origin. We compared the population structure and genetic diversity of these Vietnamese rice genomes to the 3,000 genomes of Asian cultivated rice. The named Indica-5 (I5) subpopulation was expanded in Vietnam and contained lowland Indica accessions, which had with very low shared ancestry with accessions from any other subpopulation and were previously overlooked as admixtures. We scored phenotypic measurements for nineteen traits and identified 453 unique genotype-phenotype significant associations comprising twenty-one QTLs (quantitative trait loci). The strongest associations were observed for grain size traits, while weaker associations were observed for a range of characteristics, including panicle length, heading date and leaf width. We identified genomic regions selected in both Indica and Japonica subtypes during the breeding of these subpopulations within Vietnam and discuss in detail fifty-two selected regions in I5, which constitute an untapped resource of cultivated rice diversity.Our results highlight traits and their associated genomic regions, which were identified by fine phenotyping and data integration. These are a potential source of novel loci and alleles to breed a new generation of sustainable and resilient rice.

scholarly journals Genome-wide association study for yield and yield related traits under reproductive stage drought in a diverse indica-aus rice panel

2020 ◽  
Author(s):  
Aditi Bhandari ◽  
Nitika Sandhu ◽  
Jérôme Bartholome ◽  
Tuong-Vi Cao-Hamadoun ◽  
Nourollah Ahmadi ◽  
...  
Keyword(s):  
Grain Yield ◽  
Field Experiments ◽  
Genome Wide Association Study ◽  
Agronomic Traits ◽  
Reproductive Stage ◽  
Phenotypic Variance ◽  
Rice Varieties ◽  
Drought Tolerant ◽  
Genome Wide ◽  
Genomic Regions

Abstract Background Reproductive-stage drought stress is a major impediment to rice production in rainfed areas. Conventional and marker-assisted breeding strategies for developing drought-tolerant rice varieties are being optimized by mining and exploiting adaptive traits, genetic diversity; identifying the alleles, and understanding their interactions with genetic backgrounds for their increased contribution to drought tolerance. Field experiments were conducted in this study to identify marker-trait associations (MTAs) involved in response to yield under reproductive-stage (RS) drought. A diverse set of 280 indica-aus accessions was phenotyped for ten agronomic traits including yield and yield-related traits under normal irrigated condition and under two managed reproductive-stage drought environments. The accessions were genotyped with 215,250 single nucleotide polymorphism markers. Results The study identified a total of 219 significant MTAs for 10 traits and candidate gene analysis within a 200kb window centred from GWAS identified SNP peaks detected these MTAs within/ in close proximity to 38 genes, 4 earlier reported major grain yield QTLs and 6 novel QTLs for 7 traits out of the 10. The significant MTAs were mainly located on chromosomes 1, 2, 5, 6, 9, 11 and 12 and the percent phenotypic variance captured for these traits ranged from 5 to 88%. The significant positive correlation of grain yield with yield-related and other agronomic traits except for flowering time, observed under different environments point towards their contribution in improving rice yield under drought. Seven promising accessions were identified for use in future genomics-assisted breeding programs targeting grain yield improvement under drought. Conclusion These results provide a promising insight into the complex genetic architecture of grain yield under reproductive-stage drought in different environments. Validation of major genomic regions reported in the study will enable their effectiveness to develop drought-tolerant varieties following marker-assisted selection as well as to identify genes and understanding the associated physiological mechanisms.

scholarly journals Resequencing of 672 native rice accessions to explore genetic diversity and trait associations along Vietnam

2020 ◽  
Author(s):  
Janet Higgins ◽  
Bruno Santos ◽  
Tran Dang Khanh ◽  
Khuat Huu Trung ◽  
Tran Duy Duong ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Heading Date ◽  
Cultivated Rice ◽  
Rice Varieties ◽  
Rice Landraces ◽  
Shared Ancestry ◽  
Production Areas ◽  
Genomic Regions ◽  
New Generation ◽  
Trait Associations

Abstract BACKGROUND: Vietnam possesses a vast diversity of rice landraces due to its geographical situation, latitudinal range, and a variety of ecosystems. This genetic diversity constitutes a highly valuable resource at a time when the highest rice production areas in the low-lying Mekong and Red River Deltas are enduring increasing threats from climate changes, particularly in rainfall and temperature patterns. RESULTS: We analysed 672 Vietnamese rice genomes, 616 newly sequenced, that encompass the range of rice varieties grown in the diverse ecosystems found throughout Vietnam. We described four Japonica and five Indica subpopulations within Vietnam likely adapted to the region of origin. We compared the population structure and genetic diversity of these Vietnamese rice genomes to the 3,000 genomes of Asian cultivated rice. The named Indica-5 (I5) subpopulation was expanded in Vietnam and contained lowland Indica accessions, which had with very low shared ancestry with accessions from any other subpopulation and were previously overlooked as admixtures. We scored phenotypic measurements for nineteen traits and identified 453 unique genotype-phenotype significant associations comprising twenty-one QTLs (quantitative trait loci). The strongest associations were observed for grain size traits, while weaker associations were observed for a range of characteristics, including panicle length, heading date and leaf width. CONCLUSIONS: Our results highlight differences in genome composition and trait associations among traditional Vietnamese rice accessions, which are likely the product of adaption to multiple environmental conditions and regional preferences in a very diverse country. Our results highlighted traits and their associated genomic regions that are a potential source of novel loci and alleles to breed a new generation of sustainable and resilient rice.

scholarly journals Karakter morfologi akar sebagai indikator kekurangan air pada padi lokal Superwin (Root-morphological characters as water-deficit indicators in local rice Superwin)

2014 ◽  
Vol 3 (2) ◽  
Author(s):  
Patricia Claudya Torey ◽  
Song Ai Nio ◽  
Parluhutan Siahaan ◽  
Susan M Mambu
Keyword(s):  
Oryza Sativa ◽  
Water Deficit ◽  
Upland Rice ◽  
Oryza Sativa L ◽  
Weight Ratio ◽  
Field Capacity ◽  
Dry Weight ◽  
Morphological Characters ◽  
Limited Area ◽  
Rice Varieties

Abstrak Evaluasi karakter morfologi akar telah dilakukan untuk menentukan karakter morfologi akar yang potensial sebagai indikator adanya kekurangan air pada padi (Oryza sativa L.) di antara panjang akar, volume akar, berat basah akar, berat kering akar, rasio akar:tajuk dan rasio panjang akar:tinggi tanaman. Eksperimen ini dilakukan di rumah kaca dan menggunakan 2 varietas padi (Superwin dan IR 64) pada fase vegetatif  yang ditumbuhkan pada media tanah di polybag dengan perlakuan kekeringan (tidak disirami selama 14 hari) dan disirami sampai kapasitas lapang (kontrol). Panjang akar dan rasio panjang akar:tinggi tanaman dapat dijadikan indikator kekurangan air pada padi Superwin dan IR 64. Superwin yang merupakan padi sawah dapat dipertimbangkan untuk ditanam di lahan kering. Kata kunci: indikator, kekeringan, morfologi akar Abstract Root-morphological characters in rice (Oryza sativa L.) were evaluated to determine the potential characters as water-deficit indicators among the length, volume, fresh weight, dry weight, ratio root:shoot and ratio root length:plant height. The experiment was conducted in the glasshouse using 2 rice varieties (cv. Superwin and IR 64) grown in the soil mixture at the vegetative phase. The treatments in this experiment were water deficit (without water for 14 days) and well-watered (watering until field capacity). The root length and ratio root length:plant height were potential as water- deficit indicators in Superwin dan IR 64. The upland rice, Superwin, should be considered to be cultivated in the water limited area. Keywords: drought, indicator, root morphology

Genetic diversity in agronomic traits associated with the biomass production of Miscanthus species collected in Northeast Asia

2014 ◽  
Vol 12 (S1) ◽  
pp. S137-S140 ◽  
Author(s):  
Soo-Hyun Lim ◽  
Min Jung Yook ◽  
Jin-Won Kim ◽  
Jong-Seok Song ◽  
Chuan-Jie Zhang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
East Asia ◽  
Biomass Production ◽  
Biomass Yield ◽  
Agronomic Traits ◽  
Northeast Asia ◽  
Geographical Location ◽  
Heading Date ◽  
Dry Weight ◽  
Stem Diameter

Miscanthus is a promising bioenergy crop due to its high productivity and broad environmental adaptability to tropical and temperate climates. As important Miscanthus species such as M. sinensis and M. sacchariflorus are native to East Asia, implying more diverse Miscanthus genetic resources in this region, in this study, we collected about 300 Miscanthus accessions from East Asia, mainly in Korea. From the whole collections, 66 Miscanthus accessions representing geographical location and latitude were selected and tested through a 3-year field trial to investigate genetic diversity in their agronomic traits. Five agronomic traits associated with biomass production were assessed to investigate the relationships of agronomic traits with biomass yield and latitudes of locations where Miscanthus accessions were collected. Plant height, stem diameter, stem dry weight and heading date exhibited a significantly positive correlation with biomass yield with r= 0.465, 0.780, 0.817 and 0.450, respectively. Stem diameter (r= − 0.495), stem dry weight (r= − 0.393), heading date (r= − 0.914) and estimated yield (r= − 0.425) exhibited a significantly negative correlation with latitudes of the collection sites. The results of the study revealed the existence of considerable genetic diversity in agronomic traits in the Miscanthus accessions collected. The presence of a significant relationship between latitudes and agronomic traits suggests that accessions collected from different geographical latitudes will provide more genetically diverse materials for breeding. Therefore, the results of the present study can provide useful information and materials for Miscanthus breeding programmes.

scholarly journals Karakter Agronomi Dan Satuan Panas Padi Varietas Unggul Pada Berbagai Dosis Nitrogen Di Lahan Pasang Surut

2020 ◽  
Vol 16 (1) ◽  
pp. 95
Author(s):  
Nur I. Ariyani ◽  
Dewi E. Adriani ◽  
Gusti Rusmayadi
Keyword(s):  
Plant Height ◽  
Agronomic Traits ◽  
Block Design ◽  
Dry Weight ◽  
Limiting Factor ◽  
Large Area ◽  
Rice Varieties ◽  
N Concentration ◽  
Randomized Block Design ◽  
Number Of Leaves

Rice is the staple food of Indonesian people and part of the world community. Indonesia, with a population growth rate of around 1.3-1.5% per year, requires additional rice production of about 1,8- 3 million tons of rice per year. This additional production can be achieved by using tidal swampland which is quite a large area in South Kalimantan. However, one of the obstacles in tidal swampland is the lack of nitrogen (N). N is a macronutrient that becomes the main limiting factor for plant growth as it is needed most among other nutrients. This study aimed to determine the agronomic traits of superior varieties at various N concentration. The experiment used a Split plot design with N concentration as the main plot and three rice varieties as sub-plots, while the environmental design used Randomized Block Design based on the direction of water flow. The agronomic characters observed were the number of leaves, number of tillers, plant height, the total number of panicles per plant, 1000 filled grains dry weight rice, and yield (t ha-1). The results showed that different varieties affected the plant height, number of leaves, number of tillers, the weight of 1000 grains of filled grain with IPB3S and IPB Batola 6R as the best variety, and the concentration treatment effect total of rice tillers, total of rice leaves and total number of per plant with 300 t N ha-1 as the best concentration.

scholarly journals Genetic Analysis of Root-to-Shoot Signaling and Rootstock-Mediated Tolerance to Water Deficit in Tomato

Genes ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 10
Author(s):  
Maria J. Asins ◽  
Alfonso Albacete ◽  
Cristina Martínez-Andújar ◽  
Eser Celiktopuz ◽  
İlknur Solmaz ◽  
...  
Keyword(s):  
Drought Tolerance ◽  
Water Deficit ◽  
Recombinant Inbred Lines ◽  
Xylem Sap ◽  
Climate Change Impacts ◽  
Dry Weight ◽  
Gene Families ◽  
Significant Qtls ◽  
Shoot Dry Weight ◽  
Genomic Regions

Developing drought-tolerant crops is an important strategy to mitigate climate change impacts. Modulating root system function provides opportunities to improve crop yield under biotic and abiotic stresses. With this aim, a commercial hybrid tomato variety was grafted on a genotyped population of 123 recombinant inbred lines (RILs) derived from Solanum pimpinellifolium, and compared with self- and non-grafted controls, under contrasting watering treatments (100% vs. 70% of crop evapotranspiration). Drought tolerance was genetically analyzed for vegetative and flowering traits, and root xylem sap phytohormone and nutrient composition. Under water deficit, around 25% of RILs conferred larger total shoot dry weight than controls. Reproductive and vegetative traits under water deficit were highly and positively correlated to the shoot water content. This association was genetically supported by linkage of quantitative trait loci (QTL) controlling these traits within four genomic regions. From a total of 83 significant QTLs, most were irrigation-regime specific. The gene contents of 8 out of 12 genomic regions containing 46 QTLs were found significantly enriched at certain GO terms and some candidate genes from diverse gene families were identified. Thus, grafting commercial varieties onto selected rootstocks derived from S. pimpinellifolium provides a viable strategy to enhance drought tolerance in tomato.

The study of important agronomic traits by multivariate analysis in winter rapeseed cultivars

2014 ◽  
Vol 1 (1) ◽  
pp. 20-24
Author(s):  
Gader Ghaffari ◽  
Farhad Baghbani ◽  
Behnam Tahmasebpour
Keyword(s):  
Water Potential ◽  
Water Deficit ◽  
Leaf Water Potential ◽  
Seed Weight ◽  
Dry Weight ◽  
Total Variance ◽  
Water Deficit Stress ◽  
The Third ◽  
High Eigenvalue ◽  
Winter Rapeseed

In order to group winter rapeseed cultivars according to evaluated traits, an experiment was conducted in the Research Greenhouse of Agriculture Faculty, University of Tabriz - IRAN. In the experiment were included 12 cultivars of winter rapeseed and 3 levels of water deficit stress. Gypsum blocks were used to monitor soil moisture. Water deficit stress was imposed from stem elongation to physiological maturity. According to the principal component analysis, five principal components were chosen with greater eigenvalue (more than 0.7) that are including 81.34% of the primeval variance of variables. The first component that explained the 48.02% of total variance had the high eigenvalue. The second component could justify about 13.64% of total variance and had positive association with leaf water potential and proline content and had negative relationship with leaf stomatal conductivity. The third, fourth and fifth components expressed around, 10.18, 4.83 and 4.68% of the total variance respectively. The third component had the high eigenvalue for plant dry weight. The fourth component put 1000-seed weight, seed yield, Silique per Plant and root dry weight against plant dry weight, chlorophyll fluorescence and leaf water potential. The fifth component had the high eigenvalue for root dry weight, root volume and 1000-seed weight.

scholarly journals Integration of high-density genetic mapping with transcriptome analysis uncovers numerous agronomic QTL and reveals candidate genes for the control of tillering in sorghum

2021 ◽  
Author(s):  
Rajanikanth Govindarajulu ◽  
Ashley N Hostetler ◽  
Yuguo Xiao ◽  
Srinivasa R Chaluvadi ◽  
Margarita Mauro-Herrera ◽  
...  
Keyword(s):  
Agronomic Traits ◽  
Interspecific Cross ◽  
Crop Improvement ◽  
Differentially Expressed ◽  
Plant Domestication ◽  
Sorghum Propinquum ◽  
Ril Population ◽  
Trait Locus ◽  
Genomic Regions ◽  
Low Coverage

Abstract Phenotypes such as branching, photoperiod sensitivity, and height were modified during plant domestication and crop improvement. Here, we perform quantitative trait locus (QTL) mapping of these and other agronomic traits in a recombinant inbred line (RIL) population derived from an interspecific cross between Sorghum propinquum and Sorghum bicolor inbred Tx7000. Using low-coverage Illumina sequencing and a bin-mapping approach, we generated ∼1920 bin markers spanning ∼875 cM. Phenotyping data were collected and analyzed from two field locations and one greenhouse experiment for six agronomic traits, thereby identifying a total of 30 QTL. Many of these QTL were penetrant across environments and co-mapped with major QTL identified in other studies. Other QTL uncovered new genomic regions associated with these traits, and some of these were environment-specific in their action. To further dissect the genetic underpinnings of tillering, we complemented QTL analysis with transcriptomics, identifying 6189 genes that were differentially expressed during tiller bud elongation. We identified genes such as Dormancy Associated Protein 1 (DRM1) in addition to various transcription factors that are differentially expressed in comparisons of dormant to elongating tiller buds and lie within tillering QTL, suggesting that these genes are key regulators of tiller elongation in sorghum. Our study demonstrates the usefulness of this RIL population in detecting domestication and improvement-associated genes in sorghum, thus providing a valuable resource for genetic investigation and improvement to the sorghum community.

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