Response of U.S. Rice Cultivars Grown under Non-Flooded Irrigation Management

Achieving food security along with environmental sustainability requires high yields with reduced demands on irrigation resources for rice production systems. The goal of the present investigation was to identify traits and germplasms for rice breeding programs that target effective grain production (EGP) under non-flooded field systems where the crop can be subjected to intermittent water stress throughout the growing season. A panel of 15 cultivars was evaluated over three years regarding phenological and agronomic traits under four soil moisture levels ranging from field capacity (29% volumetric water content; VWC) to just above the wilting point (16% VWC) using subsurface drip irrigation. An average of 690 ha-mm ha−1 water was applied for the 30% VWC treatment compared to 360 ha-mm ha−1 for the 14% VWC treatment. The average soil moisture content influenced several traits, including grain quality. Regression analysis identified six traits that explained 35% of the phenotypic variability of EGP. Four varieties (PI 312777, Francis, Zhe 733, and Mars) were found possessing significant slopes for 10 or more traits that respond to a range in soil moisture levels, indicating that they may offer promise for future rice breeding programs. Furthermore, based on the contrasting responses of four parent cultivars, two mapping populations were identified as potential genetic resources for identifying new quantitative trait loci/genes for improving EGP of tropical japonica rice varieties.

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Development of 454 New Kompetitive Allele-Specific PCR (KASP) Markers for Temperate japonica Rice Varieties

Plants ◽

10.3390/plants9111531 ◽

2020 ◽

Vol 9 (11) ◽

pp. 1531

Author(s):

Kyeong-Seong Cheon ◽

Young-Min Jeong ◽

Hyoja Oh ◽

Jun Oh ◽

Do-Yu Kang ◽

...

Keyword(s):

Agronomic Traits ◽

High Impact ◽

Japonica Rice ◽

Rice Varieties ◽

Breeding Programs ◽

Temperate Japonica ◽

Specific Pcr ◽

Allele Specific ◽

Allele Specific Pcr ◽

Kasp Markers

Temperate japonica rice varieties exhibit wide variation in the phenotypes of several important agronomic traits, including disease resistance, pre-harvest sprouting resistance, plant architecture, and grain quality, indicating the presence of genes contributing to favorable agronomic traits. However, gene mapping and molecular breeding has been hampered as a result of the low genetic diversity among cultivars and scarcity of polymorphic DNA markers. Single nucleotide polymorphism (SNP)-based kompetitive allele-specific PCR (KASP) markers allow high-throughput genotyping for marker-assisted selection and quantitative trait loci (QTL) mapping within closely related populations. Previously, we identified 740,566 SNPs and developed 771 KASP markers for Korean temperate japonica rice varieties. However, additional markers were needed to provide sufficient genome coverage to support breeding programs. In this study, the 740,566 SNPs were categorized according to their predicted impacts on gene function. The high-impact, moderate-impact, modifier, and low-impact groups contained 703 (0.1%), 20,179 (2.7%), 699,866 (94.5%), and 19,818 (2.7%) SNPs, respectively. A subset of 357 SNPs from the high-impact group was selected for initial KASP marker development, resulting in 283 polymorphic KASP markers. After incorporation of the 283 markers with the 771 existing markers in a physical map, additional markers were developed to fill genomic regions with large gaps between markers, and 171 polymorphic KASP markers were successfully developed from 284 SNPs. Overall, a set of 1225 KASP markers was produced. The markers were evenly distributed across the rice genome, with average marker density of 3.3 KASP markers per Mbp. The 1225 KASP markers will facilitate QTL/gene mapping and marker-assisted selection in temperate japonica rice breeding programs.

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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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Agronomic evaluation and clonal selection of ginger genotypes (Zingiber officinale Roseoe) in Brazil

Agronomía Colombiana ◽

10.15446/agron.colomb.v35n3.62454 ◽

2017 ◽

Vol 35 (3) ◽

pp. 275-284

Author(s):

Eleonora Zambrano Blanco ◽

José Baldin Pinheiro

Keyword(s):

Agronomic Traits ◽

Clonal Selection ◽

Phenotypic Variability ◽

Block Design ◽

Genetic Correlations ◽

Phenotypic Expression ◽

Germplasm Collection ◽

Environmental Variance ◽

Breeding Programs ◽

Selection Of

The analysis of the genetic diversity of ginger based on agronomic traits is essential to know its performance and to design breeding programs. In this study, we analyzed the phenotypic variability of 61 accessions of the ginger germplasm collection of the "Luiz de Queiroz" College of Agriculture at the University of Sao Paulo (ESALQ/USP) in a complete randomized block design with four replications. An analysis of variance test was performed and genetic parameters such as heritability, genetic variance, environmental variance, genetic-environmental variation ratio (CVg/CVe) and genetic correlations were estimated. There were highly significant differences (P≤0.01) among the accessions for all the agronomic traits analyzed. The CVg/CVe ratio (>1), along with the high heritability (>80%), showed a significant contribution of genetic factors on the phenotypic expression of plant height, rhizome thickness and yield traits, favoring the clonal selection of genotypes. Accessions Gen-29, Gen-29, Gen-32, Gen-36, Gen-37, Gen-40, Gen-41, Gen-42, Gen-50 were selected due to the best agronomic performance when compared to the rest of the germplasm. The results obtained may be useful in future breeding programs in Brazil.

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Analysis of Combining Ability in Rice Varieties for Quantitative Traits

Notulae Scientia Biologicae ◽

10.15835/nsb11310449 ◽

2019 ◽

Vol 11 (3) ◽

pp. 436-439

Author(s):

Ghaffar KIANI

Keyword(s):

Grain Yield ◽

Combining Ability ◽

Agronomic Traits ◽

Block Design ◽

Rice Varieties ◽

Gene Effects ◽

Breeding Programs ◽

Grain Length ◽

Additive Gene Effects ◽

Additive Gene

Rice is staple food in Iran. Despite of high quality of local rice, their grain yield is low. In hybridization breeding programs, selection of suitable parents is an essential role for developing new combinations with broadens genetic diversity. Combining ability of local rice varieties namely ‘Hashemi’, ‘Sang Jo’ and ‘Tarom Deylamani’ and ‘Nemat’ was evaluated in a partial diallele analysis for agronomic traits in a randomized complete block design at Sari Agricultural Sciences and Natural Resources University. General combining ability (GCA) and specific combining ability (SCA) variances showed predominated role of additive gene effects in the inheritance of grain length. Both additive and non-additive components of genetic variances were important in the inheritance of traits like grain yield, plant height, panicle length, total grains per panicle, grain length and grain length to width. However, non-additive gene effects were seen for tiller number. Results showed that ‘Nemat’ was the best general combiner for most of characters followed by ‘Tarom Deylamani’. The cross of ‘Hashemi’ × ‘Tarom Deylamani’ was suggested to exploitation of heterosis breeding for increasing yield and its components in rice breeding programs.

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Genotyping USDA Rice Mini-Core Collection With Functional Markers for Important Agronomic Traits

10.21203/rs.3.rs-788277/v1 ◽

2021 ◽

Author(s):

Kehu Li ◽

Yongyi Ge ◽

Lily Yan Wang

Keyword(s):

Physicochemical Properties ◽

Core Collection ◽

Biotic Resistance ◽

Agronomic Traits ◽

Brown Planthopper ◽

Functional Markers ◽

Rice Breeding ◽

Breeding Programs ◽

Exon 2 ◽

Mini Core Collection

Abstract The USDA rice mini-core collection was established to capture the diversity of an entire collection of over 18,700 accessions of global origins for efficient germplasm evaluation and exploration. Previous studies have investigated its genetic diversity and population structure using genome-wide SSR markers. Many important agronomic traits that are fundamental to rice breeding programs, however, remain to be explored. Functional markers can be developed based on polymorphic sites within genes affecting phenotypic variation in, e.g., starch physicochemical properties, nutritional qualities and biotic resistance. These markers can be used for genotyping and hence differentiating phenotypes among rice accessions. In this study, we employed 12 pairs of functional markers (SNP and Indel) to genotype all 217 accessions constituting the USDA rice mini-core. These markers are highly associated with starch physicochemical properties (intron 1 G/C SNP, 23bp duplication in exon 2, exon 6 C/A SNP, exon 10 C/T SNP of Waxy gene, GC/TT SNPs of SSIIa gene, G/C SNP of SBE3 gene), glutelin content (3.5 kb deletion in Lgc1 gene), grain length (C/A SNP in GS3 gene), brown planthopper resistance (InDel in Bph 14 gene) and rice blast resistance (InDel in Pi54 and Pit gene). Using these functional markers, all the 217 accessions of the mini-core are characterized for aforementioned agronomic traits associated alleles/genes. The results of this study will help breeders select parental materials with desirable allele/gene combinations and phenotypes among mini-core accessions for rice breeding programs.

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Performance Assessment of Five Different Soil Moisture Sensors under Irrigated Field Conditions in Oklahoma

Sensors ◽

10.3390/s18113786 ◽

2018 ◽

Vol 18 (11) ◽

pp. 3786 ◽

Cited By ~ 9

Author(s):

Sumon Datta ◽

Saleh Taghvaeian ◽

Tyson Ochsner ◽

Daniel Moriasi ◽

Prasanna Gowda ◽

...

Keyword(s):

Soil Moisture ◽

Cropping Systems ◽

Irrigation Management ◽

Clay Content ◽

Field Capacity ◽

Irrigation Scheduling ◽

Irrigated Agriculture ◽

Undisturbed Soil ◽

Soil Moisture Sensors ◽

Rosetta Model

Meeting the ever-increasing global food, feed, and fiber demands while conserving the quantity and quality of limited agricultural water resources and maintaining the sustainability of irrigated agriculture requires optimizing irrigation management using advanced technologies such as soil moisture sensors. In this study, the performance of five different soil moisture sensors was evaluated for their accuracy in two irrigated cropping systems, one each in central and southwest Oklahoma, with variable levels of soil salinity and clay content. With factory calibrations, three of the sensors had sufficient accuracies at the site with lower levels of salinity and clay, while none of them performed satisfactorily at the site with higher levels of salinity and clay. The study also investigated the performance of different approaches (laboratory, sensor-based, and the Rosetta model) to determine soil moisture thresholds required for irrigation scheduling, i.e., field capacity (FC) and wilting point (WP). The estimated FC and WP by the Rosetta model were closest to the laboratory-measured data using undisturbed soil cores, regardless of the type and number of input parameters used in the Rosetta model. The sensor-based method of ranking the readings resulted in overestimation of FC and WP. Finally, soil moisture depletion, a critical parameter in effective irrigation scheduling, was calculated by combining sensor readings and FC estimates. Ranking-based FC resulted in overestimation of soil moisture depletion, even for accurate sensors at the site with lower levels of salinity and clay.

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Submergence Gene Sub1A Transfer into Drought-Tolerant japonica Rice DT3 Using Marker-Assisted Selection

International Journal of Molecular Sciences ◽

10.3390/ijms222413365 ◽

2021 ◽

Vol 22 (24) ◽

pp. 13365

Author(s):

Yong-Pei Wu ◽

Shu-Mei Wang ◽

Yu-Chi Chang ◽

Chi Ho ◽

Yu-Chia Hsu

Keyword(s):

Good Yield ◽

Grain Quality ◽

Agronomic Traits ◽

Eating Quality ◽

Recurrent Parent ◽

High Survival ◽

Japonica Rice ◽

Rice Varieties ◽

Drought Tolerant ◽

Submergence Stress

Flash flooding is a major environmental stressor affecting rice production worldwide. DT3 is a drought-tolerant, recurrent parent with a good yield, edible quality, and agronomic traits akin to those of an elite Taiwanese variety, Taiken9 (TK9). Progenies carrying Sub1A can enhance submergence stress tolerance and can be selected using the marker-assisted backcross (MAB) breeding method. For foreground selection, Sub1A and SubAB1 were utilized as markers on the BC2F1, BC3F1, and BC3F2 generations to select the submergence-tolerant gene, Sub1A. Background selection was performed in the Sub1A-BC3F2 genotypes, and the percentages of recurrent parent recovery within individuals ranged from 84.7–99.55%. BC3F3 genotypes (N = 100) were evaluated for agronomic traits, yield, and eating quality. Four of the eleven BC3F4 lines showed good yield, yield component, grain, and eating quality. Four BC3F4 lines, SU39, SU40, SU89, and SU92, exhibited desirable agronomic traits, including grain quality and palatability, consistent with those of DT3. These genotypes displayed a high survival rate between 92 and 96%, much better compared with DT3 with 64%, and demonstrated better drought tolerance compared to IR64 and IR96321-345-240. This study provides an efficient and precise MAB strategy for developing climate-resilient rice varieties with good grain quality for flood-prone regions.

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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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Water and fertility management of rice varieties under low atmospheric evaporative demand

The Journal of Agricultural Science ◽

10.1017/s002185960002606x ◽

1970 ◽

Vol 75 (1) ◽

pp. 61-67

Author(s):

H. K. Pande ◽

Panjab Singh

Keyword(s):

Soil Moisture ◽

Life Cycle ◽

Field Capacity ◽

Evaporative Demand ◽

Rice Varieties ◽

Nitrogen Levels ◽

Fertility Management ◽

Crop Varieties ◽

Better Than ◽

Cyclic Submergence

SUMMARYFour soil moisture and two nitrogen levels were combined in eight treatments to study moisture and nitrogen effects on Dular (June–September crop) and Patnai-23 (June–November crop) varieties of rice. Both the varieties when grown under natural precipitation yielded significantly less than at other moisture levels. Whereas there were no significant differences amongst the three treatments of submergence (15–10 cm), cyclic submergence (15–0 cm) and cyclic wetting-drying (saturation to field capacity) for Dular rice, the former two treatments proved better than the latter for Patnai-23 rice. Dular responded to the treatments of cyclic wetting-drying in a way similar to that of submergence because the crop completed its life cycle during the period of low evaporative demand. Among the levels of nitrogen, 40 kg N/ha proved optimum for Dular rice and 6O kg N/ha for Patnai-23 rice. The increase in yield of grain was associated with increase in the number of panicles, number of spikelets/panicle and percentage of ripened spikelets. The concentration of N, P, Fe and Mn in the plant was maximum under submergence followed by cyclic submergence, cyclic wetting-drying and natural precipitation. Higher levels of nitrogen increased only N and P contents in the plant.

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