scholarly journals Genetic dissection of eating and cooking qualities in different subpopulations of cultivated rice (Oryza sativa L.) through association mapping

BMC Genetics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Chunfang Zhao ◽  
Ling Zhao ◽  
Qingyong Zhao ◽  
Tao Chen ◽  
Shu Yao ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Association Mapping ◽  
Genetic Factors ◽  
Amylose Content ◽  
Starch Synthesis ◽  
Cultivated Rice ◽  
Rice Varieties ◽  
Gene Markers ◽  
A Genome ◽  
Gel Consistency

Abstract Background Eating and cooking qualities (ECQs) of rice (Oryza sativa L.) determine consumer acceptance and the economic value of rice varieties. The starch physicochemical properties, i.e. amylose content, gel consistency, gelatinization temperature and pasting viscosity are important indices for evaluating rice ECQs. Genetic factors are required for development of rice varieties with excellent ECQs and association mapping is one of the promising approaches for discovering such associated genetic factors. Results A genome-wide association mapping was performed on a set of 253 non-glutinous rice accessions consisting of 83 indica and 170 japonica cultivated rice varieties through phenotyping for 11 ECQ traits in two consecutive years and genotyping with 210 polymorphic SSR and candidate-gene markers. These markers amplified 747 alleles with an average of 3.57 alleles per locus. The structure, phylogenetic relationship, and principal component analysis indicated a strong population differentiation between indica and japonica accessions and association mapping was thus undertaken within indica and japonica subpopulations. All traits showed a large phenotypic variation and highly significant phenotypic correlations were present between most of traits. A total of 33 and 30 loci were located for 11 ECQs in indica and japonica subpopulations respectively. Most of associated loci were overlapped with starch synthesis-related genes (SSRGs), and the Wx locus gathered 14 associated loci with the largest effects on amylose content, gel consistency and pasting viscosities. Eight subpopulation specific markers, RM588, Wx-(CT)n, SSI and SBE1 for indica subpopulation and RM550, Wxmp, SSIIa and SBE4 for japonica subpopulation, were identified, suggesting alleles of SSRGs showed the subspecific tendency. Nevertheless, allelic variation in SSIIa showed no tendency towards subspecies. One associated maker RM550 detected in japonica subpopulation for amylose content and pasting viscosity was verified a potential novel and stably expressed locus and could be selected for further fine mapping. Conclusion This study illustrated the potential for dissecting genetic factors of complex traits in domesticated rice subspecies and provided highly associated markers to facilitate marker-assisted selection for breeding high-quality indica or japonica rice varieties.

scholarly journals Efficacy of Irrigation Interval after Anthesis on Grain Quality, Alkali Digestion, and Gel Consistency of Rice

Agriculture ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 325
Author(s):  
Ramin Rayee ◽  
Tran Dang Xuan ◽  
Tran Dang Khanh ◽  
Hoang-Dung Tran ◽  
Kifayatullah Kakar
Keyword(s):  
Protein Content ◽  
Grain Quality ◽  
Cooking Quality ◽  
Amylose Content ◽  
Rice Grain ◽  
Gelatinization Temperature ◽  
Rice Varieties ◽  
Irrigation Interval ◽  
Gel Consistency ◽  
Alkali Digestion

The management of amylose and protein contents and cooking quality are the main challenges in rice macronutrients and quality improvement. This experiment was conducted to examine the rice grain quality, alkali digestion, and gel consistency responses to irrigation interval after anthesis. Three rice varieties (K1, K3, and K4) were subjected to different irrigation intervals (1, 2, and 3 d) after anthesis. The findings of this study showed that the protein content was markedly increased from 6.53–6.63% to 9.93–10.16%, whilst the amylose content was decreased significantly from 22.00–22.43% to 16.33–17.56% under stressed treatments at irrigation intervals, whilst the quantity of fatty acids was not affected. The 3-d irrigation interval recorded the highest protein content but the lowest amylose value. In addition, this treatment shows lower gelatinization temperature, but it is negatively associated with hard gel consistency under irrigation interval. This study highlights that the water management following a 3-d irrigation interval from anthesis is a useful and simple treatment to improve rice nutrients and grain cooking quality.

Ciri Morfologi, Fisiko-Kimia dan Kerintangan Dua Titisan Padi Kemandulan Jantan Sitoplasma (CMS) Baru

2014 ◽  
Vol 70 (6) ◽  
Author(s):  
Elixon Sunian ◽  
Mohd. Solihen Jamal ◽  
Asfaliza Ramli ◽  
Othman Omar ◽  
Habibbudin Hashim ◽  
...  
Keyword(s):  
Amylose Content ◽  
Brown Planthopper ◽  
Blast Disease ◽  
Male Sterile ◽  
Rice Varieties ◽  
Gel Consistency ◽  
Moderately Resistant ◽  
Maturation Age ◽  
B Lines ◽  
Selection Of

CMS (cytoplasmic male sterile) line is one of the most important hybrid parents in hybrid rice production technology using Three-Line systems. Test-crosses for selection of candidate local maintainer lines were conducted using 24 rice varieties and two CMS-WA (wild abortive) lines IR78374A/B and 1A/B. The F1 of the two combinations, namely IR78374A/P519 and 1A/MR243 had less than 10% spikelet fertility (6.4 and 7.2%, respectively), indicated that P519 and MR243 are partially maintainers and could be used for the development of new locally adapted CMS lines. As a results, two CMS lines, namely 0025A/B and 0047A/B were generated after 5 to 6 successive backcrossing of IR78374A with P519 and 1A with MR243. The CMS 0025A/B and 0047A/B lines had maturation age which is comparable to other commonly grown inbred varieties. The percentage of stigma exertion rate for CMS 0025A/B and 0047A/B were 17.9 and 21.3%, respectively, lower than that of IR78374A/B (43.2%). Both showed poor out-crossing rate. CMS 0025A/B and 0047A/B are classified as long and slender grain. They had intermediate amylose content. Their gel consistency was hard, comparable to that of MR263 (medium).  CMS 0025A/B and 0047A/B lines were also moderately resistant to foliar blast disease and brown planthopper infestation.

scholarly journals FLOURY ENDOSPERM19 encoding a class I glutamine amidotransferase affects grain quality in rice

2021 ◽  
Author(s):  
Guangming Lou ◽  
Pingli Chen ◽  
Hao Zhou ◽  
Pingbo Li ◽  
Jiawang Xiong ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Class I ◽  
High Yield ◽  
Eating Quality ◽  
Cultivated Rice ◽  
Rice Varieties ◽  
Rice Quality ◽  
Appearance Quality ◽  
A Genome ◽  
Glutamine Amidotransferase

Abstract As a staple food for more than half of the world’s population, the importance of rice is self-evident. Compared with ordinary rice, rice cultivars with superior eating quality and appearance quality are more popular with consumers due to its unique taste and ornamental value, even if their price is much higher. Appearance quality and CEQ (cooking and eating quality) are two very important aspects in the evaluation of rice quality. Here, we performed a genome-wide association study on chalkiness rate in a diverse panel of 533 cultivated rice accessions. We identified a batch of potential chalky genes and prioritize one (LOC_Os03g48060) for functional analyses. Two floury outer endosperm mutants (flo19-1 and flo19-2) were generated through editing LOC_Os03g48060 (named as FLO19 in this study), which encodes a class I glutamine amidotransferase. The different performance of the two mutants in various storage substances directly led to completely different changes in CEQ. The mutation of FLO19 gene caused the damage of carbon and nitrogen metabolism in rice, which affected the normal growth and development of rice, including decreased plant height and yield loss by decreased grain filling rate. Through haplotype analysis, we identified a haplotype of FLO19 that can improve both CEQ and appearance quality of rice, Hap2, which provides a selection target for rice quality improvement, especially for high-yield indica rice varieties.

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 Sequence variations in OsAGPase significantly associated with amylose content and viscosity properties in rice (Oryza sativa L.)

2012 ◽  
Vol 94 (4) ◽  
pp. 179-189 ◽  
Author(s):  
FU-HAO LU ◽  
YONG-JIN PARK
Keyword(s):  
Oryza Sativa ◽  
Linear Model ◽  
Amylose Content ◽  
Oryza Sativa L ◽  
Starch Synthesis ◽  
Eating Quality ◽  
Nucleotide Polymorphisms ◽  
Small Unit ◽  
Sequence Variations ◽  
Population Structure Analysis

SummarySequence-based variations in starch synthesis-related genes (SSRGs) exert a basic influence on the determination of eating quality in rice (Oryza sativa L.). This study aimed to investigate the relationship between the sequence variations from parts of 10 SSRGs and the amylose content (AC) plus rapid viscosity analysis (RVA) profiles in a heuristic rice core set by association mapping (AM). In total, 86 sequence variations were found in 10 sequenced amplicons, including 79 single-nucleotide polymorphisms (SNPs), six insertion-deletions (InDels) and one polymorphic simple sequence repeat (SSR). Among them, 61 variations were exon-based, of which 41 should lead to amino acid changes. Four subpopulations were revealed by population structure analysis based on 170 genome-wide SSR genotypes. The final AM showed a sum of four significant associations between three phenotypic indices and three sequence variations. An ADP-glucose pyrophosphorylase small unit 1 (OsAGPS1) SNP (A–G) was significantly associated with increased AC (P<0·001, R2=15·6%), while a 12-bp deletion of AGPase large unit 4 (OsAGPL4) was significantly related to the decreased breakdown viscosity (BDV) (P<0·001, R2=16·6%) in both general linear model (GLM) and mixed linear model (MLM). This study provides a new perspective of allele mining for breeding strategies based on marker-assisted selection.

scholarly journals Glycemic index studies in rice (Oryza sativa L.) varieties developed by ANGRAU

2021 ◽  
Vol 17 (AAEBSSD) ◽  
pp. 133-137
Author(s):  
S. Divya Prasanna Kumari ◽  
G. Nirmala Devi ◽  
N. Chamundeswari
Keyword(s):  
Glycemic Index ◽  
Significant Variation ◽  
Agricultural Research ◽  
Amylose Content ◽  
Oryza Sativa L ◽  
Research Station ◽  
Rice Varieties ◽  
Gel Consistency ◽  
The Mean ◽  
Chemical Traits

Twenty popular rice varieties developed by ANGRAU obtained from Regional Agricultural Research Station (RARS), Maruteru during Kharif – 2019, were screened for chemical quality traits viz., gel consistency, gelatinization temperature, amylose along with glycemic index.In our study, significant variation was observed among all the varieties for chemical traits but no significant variation was observed in case of glycemic index.The amylose content observed over the varieties ranged from 21.7 per cent to 24.73 per cent. All the varieties have intermediate amylose content. Gel consistency ranged from 37.67 (hard gel) to 75 (soft gel) with the mean of 52.57. The alkali spreading value was noticed to be low, intermediate and high among all rice varieties.Glycemic index rangedfrom 56.72 -66.43 with a general mean of 60.67. Furthermore, all the varieties were categorized as medium GI varieties (56-69). Among all the varieties, Pushyami has shown the least value (56.72) for glycemic index.From the present investigation, it is concluded that, Rice varieties such as Chandra, Indra, Sri Dhruthi, Swarna, Samba Mahsuri, Sujatha, Maruteru Samba, MaruteruMahsuri recorded intermediate amylose, alkali spreading value and medium GI, which are desirable for rice consumers while counting for better rice with the best quality and glycemic index.

scholarly journals A large-scale analysis of seed natural aging revealed stronger aging resistance in weedy rice than coexisting cultivated rice for continuous 4 years across China

2019 ◽  
Author(s):  
weimin dai ◽  
Yuan Wang ◽  
Yu-Jie Zhang ◽  
Xi-Xi Sun ◽  
Jin-Ling Yang ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Large Scale ◽  
Oryza Sativa L ◽  
Germination Rate ◽  
Weedy Rice ◽  
Japonica Rice ◽  
Rice Cultivars ◽  
Cultivated Rice ◽  
Rice Varieties ◽  
Aging Resistance

Abstract Increasing resistance to aging is conducive to seed storage and germination rate of crop. Meanwhile, the resistance to aging is one of the important adaptive mechanisms of weed to thrive in farmland. Weedy rice (Oryza sativa f. spontanea) and cultivated rice (Oryza sativa L.) provide a unique pair demonstrating a weed and conspecific model crop that can be used to study the aging resistance of plants across a diverse geographical range. Chinese weedy rice derived from de-domestication of cultivated rice has rapidly risen to malignant weeds, though the hazard has only been reported for about 20 years. Whether weedy rice rapidly evolves higher seed aging resistance than cultivated rice during the process of dedomestication, which is conducive to its persistence in rice fields, is still unclear. In this experiment, the seeds of weed rice populations and their co-existing rice varieties were collected from 61 regions of China and germinated under normal and high temperatures for consecutive four years (2013–2016). Our study found that the aging resistance of weedy rice was higher than that of the co-existing rice cultivars, and weedy rice may have evolved a different aging resistance mechanism than rice cultivars and could be used as a germplasm resource to cultivate aging-resistant rice. The indica-type has strong aging resistance and no dormancy, while the japonica type has weak aging resistance and a little weak dormancy. Thus, by introducing indica-type aging-resistant alleles into japonica rice, cultivation of aging-resistant japonica rice could be possible.

scholarly journals Relationship between High Temperature and Formation of Chalkiness and Their Effects on Quality of Rice

2018 ◽  
Vol 2018 ◽  
pp. 1-18 ◽  
Author(s):  
A. Y. M. Nevame ◽  
R. M. Emon ◽  
M. A. Malek ◽  
M. M. Hasan ◽  
Md. Amirul Alam ◽  
...  
Keyword(s):  
High Temperature ◽  
Amylose Content ◽  
Pragmatic Approach ◽  
Rice Varieties ◽  
Material Resources ◽  
Temperature Responsive ◽  
Stable Qtls ◽  
Gel Consistency ◽  
Genetic And Environmental Factors

Occurrence of chalkiness in rice is attributed to genetic and environmental factors, especially high temperature (HT). The HT induces heat stress, which in turn compromises many grain qualities, especially transparency. Chalkiness in rice is commonly studied together with other quality traits such as amylose content, gel consistency, and protein storage. In addition to the fundamental QTLs, some other QTLs have been identified which accelerate chalkiness occurrence under HT condition. In this review, some of the relatively stable chalkiness, amylose content, and gel consistency related QTLs have been presented well. Genetically, HT effect on chalkiness is explained by the location of certain chalkiness gene in the vicinity of high-temperature-responsive genes. With regard to stable QTL distribution and availability of potential material resources, there is still feasibility to find out novel stable QTLs related to chalkiness under HT condition. A better understanding of those achievements is essential to develop new rice varieties with a reduced chalky grain percentage. Therefore, we propose the pyramiding of relatively stable and nonallelic QTLs controlling low chalkiness endosperm into adaptable rice varieties as pragmatic approach to mitigate HT effect.

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