scholarly journals Genetic analysis of rice seedling traits related to machine transplanting under different seeding densities

2020 ◽  
Author(s):  
Dan Zhu ◽  
Yuping Zhang ◽  
Jing Xiang ◽  
Yaliang Wang ◽  
Defeng Zhu ◽  
...  
Keyword(s):  
Stress Responses ◽  
Cropping Systems ◽  
Indica Rice ◽  
Dry Weight ◽  
Rice Seedling ◽  
Seeding Density ◽  
Japonica Rice ◽  
Rice Varieties ◽  
Seedling Traits ◽  
Ril Population

Abstract Background: Due to the diversity of rice varieties and cropping systems in China, the limitation of seeding density and seedling quality makes it hard to improve machine-transplanted efficiency. Previous studies have shown that indica and japonica varieties varied in machine transplanting efficiency and optimal seeding density . In this study, a RIL population derived from ‘9311’ and ‘ Nipponbare ’ were performed to explore the seedling traits variations and the genetic mechanism under three seeding densities. Results: The parents and RIL population exhibited similar trends as the seeding density increased, including seedling height and first leaf sheath length increases, shoot dry weight and root dry weight decreases. Among the 37 QTLs for six traits detected under the three seeding densities, 12 QTLs were detected in both three seeding densities. Five QTL hotspots identified clustered within genomic regions on chromosomes 1, 2, 4, 6 and 11. Specific QTLs such as qRDW 1.1 and qFLSL 5.1 were detected under low and high seeding densities, respectively. Detailed analysis the QTL regions identified under specific seeding densities revealed several candidate genes involved in phytohormones signals and abiotic stress responses. Whole-genome additive effects showed that ‘9311’ contributed more loci enhancing trait performances than ‘Nipponbare’, indicating ‘9311’ was more sensitive to the seeding density than ‘Nipponbare’. The prevalence of negative epistasis effects indicated that the complementary two-locus homozygotes may not have marginal advantages over the means of the two parental genotypes. Conclusions: Our results revealed the differences between indica rice and japonica rice seedling traits in response to seeding density. Several QTL hotspots involved in different traits and specific QTLs (such as qRDW 1.1 and qFLSL 5.1 ) in diverse seeding densities had been detected. Genome-wide additive and two-locus epistasis suggested a dynamic of the genetic control underlying different seeding densities. It was concluded that novel QTLs, additive and epistasis effects under specific seeding density would provide adequate information for rice seedling improvement during machine transplanting.

scholarly journals Genetic analysis of rice seedling traits related to machine transplanting under different seeding densities

BMC Genetics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Dan Zhu ◽  
Yuping Zhang ◽  
Jing Xiang ◽  
Yaliang Wang ◽  
Defeng Zhu ◽  
...  
Keyword(s):  
Stress Responses ◽  
Cropping Systems ◽  
Indica Rice ◽  
Dry Weight ◽  
Rice Seedling ◽  
Seeding Density ◽  
Japonica Rice ◽  
Rice Varieties ◽  
Seedling Traits ◽  
Ril Population

Abstract Background Due to the diversity of rice varieties and cropping systems in China, the limitation of seeding density and seedling quality makes it hard to improve machine-transplanted efficiency. Previous studies have shown that indica and japonica varieties varied in machine transplanting efficiency and optimal seeding density. In this study, a RIL population derived from ‘9311’ and ‘Nipponbare’ were performed to explore the seedling traits variations and the genetic mechanism under three seeding densities. Results The parents and RIL population exhibited similar trends as the seeding density increased, including seedling height and first leaf sheath length increases, shoot dry weight and root dry weight decreases. Among the 37 QTLs for six traits detected under the three seeding densities, 12 QTLs were detected in both three seeding densities. Five QTL hotspots identified clustered within genomic regions on chromosomes 1, 2, 4, 6 and 11. Specific QTLs such as qRDW1.1 and qFLSL5.1 were detected under low and high seeding densities, respectively. Detailed analysis the QTL regions identified under specific seeding densities revealed several candidate genes involved in phytohormones signals and abiotic stress responses. Whole-genome additive effects showed that ‘9311’ contributed more loci enhancing trait performances than ‘Nipponbare’, indicating ‘9311’ was more sensitive to the seeding density than ‘Nipponbare’. The prevalence of negative epistasis effects indicated that the complementary two-locus homozygotes may not have marginal advantages over the means of the two parental genotypes. Conclusions Our results revealed the differences between indica rice and japonica rice seedling traits in response to seeding density. Several QTL hotspots involved in different traits and specific QTLs (such as qRDW1.1 and qFLSL5.1) in diverse seeding densities had been detected. Genome-wide additive and two-locus epistasis suggested a dynamic of the genetic control underlying different seeding densities. It was concluded that novel QTLs, additive and epistasis effects under specific seeding density would provide adequate information for rice seedling improvement during machine transplanting.

scholarly journals Genetic analysis of rice seedling traits related to machine transplanting under different seeding densities

2020 ◽  
Author(s):  
Dan Zhu ◽  
Yuping Zhang ◽  
Jing Xiang ◽  
Yaliang Wang ◽  
Defeng Zhu ◽  
...  
Keyword(s):  
Stress Responses ◽  
Cropping Systems ◽  
Indica Rice ◽  
Dry Weight ◽  
Rice Seedling ◽  
Seeding Density ◽  
Japonica Rice ◽  
Rice Varieties ◽  
Seedling Traits ◽  
Ril Population

Abstract Background: Due to the diversity of rice varieties and cropping systems in China, the limitation of seeding density and seedling quality makes it hard to improve machine-transplanted efficiency. Previous studies have shown that indica and japonica varieties varied in machine transplanting efficiency and optimal seeding density. In this study, a RIL population derived from ‘9311’ and ‘Nipponbare’ were performed to explore the seedling traits variations and the genetic mechanism under three seeding densities. Results: The parents and RIL population exhibited similar trends as the seeding density increased, including seedling height and first leaf sheath length increases, shoot dry weight and root dry weight decreases. Among the 37 QTLs for six traits detected under the three seeding densities, 12 QTLs were detected in both three seeding densities. Five QTL hotspots identified clustered within genomic regions on chromosomes 1, 2, 4, 6 and 11. Specific QTLs such as qRDW1.1 and qFLSL5.1 were detected under low and high seeding densities, respectively. Detailed analysis the QTL regions identified under specific seeding densities revealed several candidate genes involved in phytohormones signals and abiotic stress responses. Whole-genome additive effects showed that ‘9311’ contributed more loci enhancing trait performances than ‘Nipponbare’, indicating ‘9311’ was more sensitive to the seeding density than ‘Nipponbare’. The prevalence of negative epistasis effects indicated that the complementary two-locus homozygotes may not have marginal advantages over the means of the two parental genotypes. Conclusions: Our results revealed the differences between indica rice and japonica rice seedling traits in response to seeding density. Several QTL hotspots involved in different traits and specific QTLs (such as qRDW1.1 and qFLSL5.1) in diverse seeding densities had been detected. Genome-wide additive and two-locus epistasis suggested a dynamic of the genetic control underlying different seeding densities. It was concluded that novel QTLs, additive and epistasis effects under specific seeding density would provide adequate information for rice seedling improvement during machine transplanting.

scholarly journals Genetic analysis of rice seedling traits related to machine transplanting under different seeding densities

2020 ◽  
Author(s):  
Dan Zhu ◽  
Yuping Zhang ◽  
Jing Xiang ◽  
Yaliang Wang ◽  
Defeng Zhu ◽  
...  
Keyword(s):  
Stress Responses ◽  
Cropping Systems ◽  
Indica Rice ◽  
Dry Weight ◽  
Rice Seedling ◽  
Seeding Density ◽  
Japonica Rice ◽  
Rice Varieties ◽  
Seedling Traits ◽  
Ril Population

Abstract Background: Due to the diversity of rice varieties and cropping systems in China, the limitation of seeding density and seedling quality makes it hard to improve machine-transplanted efficiency. Previous studies have shown that indica and japonica varieties varied in machine transplanting efficiency and optimal seeding density. In this study, a RIL population derived from ‘9311’ and ‘Nipponbare’ were performed to explore the seedling traits variations and the genetic mechanism under three seeding densities. Results: The parents and RIL population exhibited similar trends as the seeding density increased, including seedling height and first leaf sheath length increases, shoot dry weight and root dry weight decreases. Among the 37 QTLs for six traits detected under the three seeding densities, 12 QTLs were detected in both three seeding densities. Five QTL hotspots identified clustered within genomic regions on chromosomes 1, 2, 4, 6 and 11. Specific QTLs such as qRDW1.1 and qFLSL5.1 were detected under low and high seeding densities, respectively. Detailed analysis the QTL regions identified under specific seeding densities revealed several candidate genes involved in phytohormones signals and abiotic stress responses. Whole-genome additive effects showed that ‘9311’ contributed more loci enhancing trait performances than ‘Nipponbare’, indicating ‘9311’ was more sensitive to the seeding density than ‘Nipponbare’. The prevalence of negative epistasis effects indicated that the complementary two-locus homozygotes may not have marginal advantages over the means of the two parental genotypes. Conclusions: Our results revealed the differences between indica rice and japonica rice seedling traits in response to seeding density. Several QTL hotspots involved in different traits and specific QTLs (such as qRDW1.1 and qFLSL5.1) in diverse seeding densities had been detected. Genome-wide additive and two-locus epistasis suggested a dynamic of the genetic control underlying different seeding densities. It was concluded that novel QTLs, additive and epistasis effects under specific seeding density would provide adequate information for rice seedling improvement during machine transplanting.

Geographic pattern of variation among Asian native rice cultivars (Oryza sativa L.) based on fifteen isozyme loci

Genome ◽  
1988 ◽  
Vol 30 (5) ◽  
pp. 782-792 ◽  
Author(s):  
J. C. Glaszmann
Keyword(s):  
Genetic Diversity ◽  
Oryza Sativa ◽  
Oryza Sativa L ◽  
Indian Subcontinent ◽  
Indica Rice ◽  
Japonica Rice ◽  
Geographic Pattern ◽  
Cultivated Rice ◽  
Rice Varieties ◽  
Himalayan Foothills

The geographic pattern of isozyme variation among rice varieties (Oryza sativa L.) in Asia is described based on an electrophoretic survey of 1688 accessions for 15 loci. The distribution patterns are strongly determined by the existence of several varietal groups that are characterized by contrasting multilocus types with dissimilar environmental and macrogeographic distributions. The two main groups correspond to the indica and japonica subspecies. Other types are frequently found in the Indian subcontinent, especially along the Himalayan foothills. These types are predominant in the Indus River basin. They are differentiated into four groups in the eastern part of the Himalayan foothills. There is variation within the groups. Non-random allele distributions are observed, such as regional clines and narrow localization of alleles. Diversity among indica rice is evenly distributed in whole tropical Asia. Variation among japonica rice shows the hilly part of continental Southeast Asia to be the region of highest genetic diversity and its probable area of origin. All this information provides a guide for further analysis aimed at elucidating the history of cultivated rice in Asia and, subsequently, in other continents.Key words: Asian rice, genetic diversity, isozymes, geographic distributions.

scholarly journals Screening and Expression of a Silicon Transporter Gene(Lsi1)in Wild-Type Indica Rice Cultivars

2017 ◽  
Vol 2017 ◽  
pp. 1-13 ◽  
Author(s):  
Mahbod Sahebi ◽  
Mohamed M. Hanafi ◽  
M. Y. Rafii ◽  
Parisa Azizi ◽  
Rambod Abiri ◽  
...  
Keyword(s):  
Antioxidant Activities ◽  
Indica Rice ◽  
Rice Variety ◽  
Morphological Properties ◽  
Japonica Rice ◽  
Wild Type ◽  
Rice Varieties ◽  
Silicon Transporter ◽  
Chlorophyll A And B ◽  
Japonica Rice Variety

Silicon (Si) is one of the most prevalent elements in the soil. It is beneficial for plant growth and development, and it contributes to plant defense against different stresses. TheLsi1gene encodes a Si transporter that was identified in a mutant Japonica rice variety. This gene was not identified in fourteen Malaysian rice varieties during screening. Then, a mutant version ofLsi1was substituted for the native version in the three most common Malaysian rice varieties, MR219, MR220, and MR276, to evaluate the function of the transgene. Real-time PCR was used to explore the differential expression ofLsi1in the three transgenic rice varieties. Silicon concentrations in the roots and leaves of transgenic plants were significantly higher than in wild-type plants. Transgenic varieties showed significant increases in the activities of the enzymes SOD, POD, APX, and CAT; photosynthesis; and chlorophyll content; however, the highest chlorophyll A and B levels were observed in transgenic MR276. Transgenic varieties have shown a stronger root and leaf structure, as well as hairier roots, compared to the wild-type plants. This suggests thatLsi1plays a key role in rice, increasing the absorption and accumulation of Si, then alters antioxidant activities, and improves morphological properties.

scholarly journals Construction of vector and transformation of drought-responsive gene OsNAC1 into J02 (Oryza sativa L. Japonica) rice

2016 ◽  
Vol 14 (2) ◽  
pp. 271-277
Author(s):  
Phạm Thu Hằng ◽  
Đàm Quang Hiếu ◽  
Phan Tuấn Nghĩa ◽  
Phạm Xuân Hội
Keyword(s):  
Transcription Factor ◽  
Oryza Sativa ◽  
Stress Responses ◽  
Transcriptional Activation ◽  
Oryza Sativa L ◽  
Terminal Region ◽  
Cauliflower Mosaic Virus ◽  
Japonica Rice ◽  
Rice Varieties ◽  
Gm Plants

NAC (including NAM - no apical meristem, ATAF1/2 - Arabidopsis transcription activation factor and CUC2 - cup-shaped cotyledon), which is the largest plant transcription factor family, plays an important role in development and stress responses in plants. Protein of this family is characterized by a highly conserved DNA binding domain, known as NAC domain in the N-terminal region. In contrast, the C-terminal region of NAC proteins, usually containing the transcriptional activation domain, is highly diversified both in length and sequence. More than 100 members of this family have been identified in rice. However, only a few of them have been functionally characterized, especially in rice. Gene encoding transcription factor OsNAC1 has been proved to play an important role in drought stress in plants. The CaMV35S promoter derived from the common plant virus, cauliflower mosaic virus (CaMV), is a component of transgenic constructs in more than 80% of genetically modified (GM) plants. It is the promoter of choice for plant genetic engineering, as it is a strong and constitutive promoter. In this study, an expression vector harboring OsNAC1 in the form of CaMV35S:OsNAC1:Nos was constructed and transferred into J02 (Oryza sativa L. Japonica) rice plants via Agrobacterium tumefaciens. The presence of the transgene was confirmed by PCR using OsNAC1 specific primers. T0 CaMV35S:OsNAC1:Nos transgenic lines were selected from transgenic plants. The obatained results are expected to be further exploited for development of stress tolerant rice varieties in the future.

scholarly journals Mapping of quantitative trait loci for purple stigma and purple apiculus in rice by using a Zhenshan 97B/Minghui 63 RIL population

2021 ◽  
Author(s):  
Jiping Tong ◽  
Zhengshu Han ◽  
Aonan Han
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Indica Rice ◽  
Phenotypic Variance ◽  
Chromosome 6 ◽  
Rice Varieties ◽  
Morphological Marker ◽  
Ril Population ◽  
Trait Loci ◽  
Major Qtl

Anthocyanin pigmentation is an important morphological marker that is commonly used to identify rice varieties and for linkage analysis. The following study investigates the genetic factors involved in the purple stigma (Ps) and purple apiculus (Pa) traits of an important indica rice cross between Zhenshan 97 (purple stigma and purple apiculus) and Minghui 63 (grey stigma and colourless apiculus). A recombinant inbred line (RIL) population derived from this cross was used for quantitative trait loci (QTL) mapping of the purple stigma and purple apiculus traits. As a result, one major QTL for the purple stigma trait, temporarily designated qPS-1-1, and one major QTL for the purple apiculus trait, temporarily designated qPA-1-1, were mapped to the short arm of chromosome 6 in the interval between the two markers Y4073L and *P. The LOD peaks of qPS-1-1 and qPA-1-1 were 44.0127 and 173.3585, respectively. In addition, qPS-1-1 and qPA-1-1 explained 66.7416% and 98.6441% of the total phenotypic variance, respectively. The Zhenshan 97 allele increased the purple stigma trait by approximately 8.0355% (for qPS-1-1) and 9.8863% (for qPA-1-1). Moreover, since qPS-1-1 and qPA-1-1 were strongly correlated, they were also located in the same vicinity of the C gene on the short arm of chromosome 6, which suggested that the two QTL might be the same. By comparing these and previous results, it was deduced that qPS-1-1 or qPA-1-1 was the C gene and was pleiotropic for both the colouration of the apiculus and the colouration of the stigma in rice.

scholarly journals Impacts of rice varieties and management on yield-scaled greenhouse gas emissions from rice fields in China: A meta-analysis

2014 ◽  
Vol 11 (13) ◽  
pp. 3685-3693 ◽  
Author(s):  
H. Zheng ◽  
H. Huang ◽  
L. Yao ◽  
J. Liu ◽  
H. He ◽  
...  
Keyword(s):  
Greenhouse Gas ◽  
Indica Rice ◽  
Meta Analysis ◽  
Ghg Emissions ◽  
Cropping System ◽  
Japonica Rice ◽  
Growth Duration ◽  
Rice Varieties ◽  
System A ◽  
Unit Yield

Abstract. Increasing numbers of studies have suggested that a comprehensive assessment of the impacts of cropping practices on greenhouse gas (GHG) emissions per unit yield (yield-scaled), rather than by land area (area-scaled), is needed to inform trade-off decisions to increase yields and reduce GHG emissions. We conducted a meta-analysis to quantify impacts of rice varieties on the global warming potential (GWP) of GHG emissions at the yield scale in China. Our results showed that significantly higher yield-scaled GWP occurred with indica rice varieties (1101.72 kg CO2 equiv. Mg−1) than japonica rice varieties (711.38 kg CO2 equiv. Mg−1). Lower yield-scaled GHG emissions occurred within 120–130 days of growth duration after transplanting (GDAT; 613.66 kg CO2 equiv. Mg−1), followed by 90–100 days of GDAT (749.72 kg CO2 equiv. Mg−1, 100–110 days of GDAT (794.29 kg CO2 equiv. Mg−1), and 70–80 days of GDAT (800.85 kg CO2 equiv. Mg−1). The fertilizer rate of 150–200 kg N ha−1 resulted in the lowest yield-scaled GWP. Consequently, appropriate cultivar choice and pairs were of vital importance in the rice cropping system. A further life cycle assessment of GHG emissions among rice varieties at the yield scale is urgently needed to develop win–win policies for rice production to achieve higher yield with lower emissions.

scholarly journals Identifikasi dan Aplikasi Marka Berbasis PCR untuk Identifikasi Varietas Padi dengan Palatabilitas Tinggi

2016 ◽  
Vol 8 (2) ◽  
pp. 69 ◽  
Author(s):  
Puji Lestari ◽  
Andari Risliawati ◽  
Hee Jong Koh
Keyword(s):  
Molecular Markers ◽  
Indica Rice ◽  
Rice Variety ◽  
Dna Fingerprint ◽  
Eating Quality ◽  
Japonica Rice ◽  
Rice Varieties ◽  
Genome Database ◽  
Value System ◽  
Unique Identity

<p>To date, there has<br />been no DNA fingerprint profile as unique identity of rice<br />variety that has a high palatability (overall eating quality) in<br />Indonesia, thus identification of premium varieties using<br />molecular markers is considered to be important. This study<br />aimed to establish DNA fingerprint profiles of indica and<br />japonica rice varieties, and unique identities of rice varieties<br />with high palatability using molecular markers associated<br />with palatability. Total of 22 japonica and 24 indica rice<br />varieties were evaluated their overall eating quality and<br />tested using 20 molecular markers STS (sequence-tagged<br />site) which were designed on the basis of japonica rice<br />genome. To identify the genes functions, all these markers<br />amplicons were cloned, transformed, sequenced and the<br />sequences results were analyzed their homologous against<br />the genome database. Ilpum (japonica) and Rojolele<br />(indica) were identified to have the highest palatability<br />compared to other varieties. DNA fingerprint profiles<br />identified with the total STS markers were not able to<br />differentiate each variety, however premium varieties of<br />japonica and indica showed specific identities. A unique<br />identity of Indonesian indica variety possessing high<br />palatability, Rojolele was successfully developed using a<br />markers set. DNA fingerprint profile in digital value system<br />facilitates the identification of premium rice from other<br />varieties. The fragments of the STS primers showed no any<br />known-genes functions related to rice eating quality,<br />therefore these markers are preferentially used for<br />identification of premium rice with high palatability than<br />differentiation of rice varieties based on the palatability. In<br />this study, the unique identity of rice variety with high<br />palatability is very usefull to evaluate the purity for<br />germplasm protection.</p>

scholarly journals Impacts of rice varieties and management on yield-scaled greenhouse gas emissions from rice fields in China: a meta-analysis

2013 ◽  
Vol 10 (12) ◽  
pp. 19045-19069 ◽  
Author(s):  
H. Zheng ◽  
H. Huang ◽  
L. Yao ◽  
J. Liu ◽  
H. He ◽  
...  
Keyword(s):  
Greenhouse Gas ◽  
Indica Rice ◽  
Meta Analysis ◽  
Ghg Emissions ◽  
Cropping System ◽  
Japonica Rice ◽  
Growth Duration ◽  
Rice Varieties ◽  
System A ◽  
Unit Yield

Abstract. Increasing numbers of studies have suggested that a comprehensive assessment of the impacts of cropping practices on greenhouse gas (GHG) emissions per unit yield (yield-scaled), rather than by land area (area-scaled), is needed to inform trade-off decisions to increase yields and reduce GHG emissions. We conducted a meta-analysis to quantify impacts of rice varieties on the global warming potential (GWP) of GHG emissions at the yield scale in China. The results showed that significantly higher yield-scaled GWP occurred with indica rice varieties (1101.72 kg CO2 equiv. Mg−1) compared to japonica rice varieties (711.38 kg CO2 equiv. Mg−1). Lower yield-scaled GHG emissions occurred within 120–130 days of growth duration after transplanting (GDAT; 613.66 kg CO2 equiv. Mg−1), followed by 90–100 days of GDAT (749.72 kg CO2 equiv. Mg−1), 100–110 days of GDAT (794.29 kg CO2 equiv. Mg−1), and 70–80 days of GDAT (800.85 kg CO2 equiv. Mg−1). The greatest reduction, 41%, occurred at a rate of 150–200 kg N ha−1 relative to the non-fertilized control. Consequently, appropriate cultivar choice and pairs was of vital importance in the rice cropping system. A further life cycle assessment of GHG emissions among rice varieties at the yield scale is urgently needed to develop win–win policies for rice production to achieve higher yield with lower emissions.

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