Mapping quantitative trait loci associated with starch paste viscosity in rice (<i>Oryza sativa</i> L.) under different environmental conditions

Yao, Xingdong; Wang, Jiayu; Jin, Liu; Jia, Zhang; Ren, Chen-Xi; Ma, Dianrong; Xu, Hai Jun; Xu, Zhenbo

doi:10.1111/pbr.12505

Cited by 11 publications

(20 citation statements)

References 51 publications

(83 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Other loci for RVA parameters associated with SSR markers were detected in individual subpopulation and only in 1 year, which distributed on Chr.1, 4, 7, 8, 9 and 10. The accuracy of these loci needs to be verified in future, even though most of them have been identified in natural or linkage populations based on different genetic background [ 15 , 37 – 39 ].…”

Section: Discussionmentioning

confidence: 99%

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

Zhao

QingYong

et al. 2020

BMC Genet

View full text Add to dashboard Cite

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.

show abstract

Section: Discussionmentioning

confidence: 99%

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

Zhao

QingYong

et al. 2020

BMC Genet

View full text Add to dashboard Cite

show abstract

“…These traits were not measured in the RIL population in this current study; however, the results revealed among the 106 diverse varieties signal existing associations between TPA traits and AAC (Table 4.2). Despite these presence of large-effect QTLs and results corroborating with previous studies (Bao et al, 2000, Yao et al, 2017, the drawback in this current QTL mapping effort is the absence of environmental factor;…”

Section: Qtls For Aac and Rva Traits In The Populationsupporting

confidence: 86%

Understanding the genetics and chemistry of important quality traits in rice (Oryza sativa L.)

Concepcion¹

View full text Add to dashboard Cite

Rice grain quality is a determinant of rice breeding success. Although several studies have independently looked at the different traits of quality to infer the phenotype of the grain, few studies have identified the various metabolites that are produced in high quality rice. In recent years, genetic markers have proven to be effective in increasing the efficiency of breeding line selection and therefore shortening the breeding cycle. In complex traits such as rice grain quality, the availability of more specific phenotypes will increase the value of these genetic markers. Many traits of quality in rice are associated with starch; however, lipids interact with starch and have been shown to influence many of the traits of eating quality and aroma. To identify these new phenotypes and understand their genetic basis, using relevant tools that can discriminate between the phenotypes of varieties at the metabolite and genetic levels is necessary. To identify these new phenotypes, in Chapter 3, a set of 40 Cambodian rice varieties were screened for physical and texture-associated traits including apparent amylose content (AAC), gelatinisation temperature (GT), gel consistency (GelCon) and pasting properties and then a subset from this set was screened for volatile compounds using a two-dimensional gas chromatography-time-of-flightmass spectrometer (GC×GC-TOF-MS) and fatty acids (FA) using gas chromatography-mass spectrometry (GC-MS). The FA analysis showed that unsaturated FA (UFA) oleic (C18:1n-9) and linoleic acid (C18:2n-6) were the most abundant in milled rice grains, followed by palmitic acid (C16:0). These results infer about the lipid origin of odour-active volatile compounds, which were found to be characterising the group of known fragrant, low amylose and soft-textured rice varieties, including the Jasmine-style indica variety Phka Rumduol (PRD). To identify the genetic determinants of these important traits of quality, in Chapters 4 and 5, quantitative trait loci (QTL) mapping was carried out for the texture and aroma traits in PRD using a population of about 300 F6 recombinant-inbred lines (RIL) derived from an intraspecific cross between PRD and Thmar Krem (TMK), both of which were identified as the most discriminating varieties in Chapter 3. This RIL population was genotyped for single nucleotide polymorphisms (SNPs). QTL analysis revealed large-effect QTLs for AAC, GT and all of the pasting properties. Candidate genes for these QTLs relate back to the starch biosynthesis pathways. Major QTLs were colocalised to the Waxy (Wx) gene and starch synthase IIa (SSIIa) on chromosome 6. Minor QTLs on chromosomes 3 and 8 were identified for AAC, SB, PV and HPC, and at chromosomes 4 and 7 for GT and pasting temperature (PTemp). This chapter has shown that the rice texture is regulated by multiple genes and that although correlations do exist among the routinely measured textural traits, these correlations may not necessarily translate into the already existing molecular markers. Publications included in this thesis...

show abstract

“…More than 200 starch RVA trait QTLs were localized using various mapping populations [3,6,[17][18][19][20][21][22][23]. A few QTLs have been cloned or subjected to ne-mapping (http://www.gramene.org/, http://www.ricedata.cn/).…”

Section: Introductionmentioning

confidence: 99%

“…Certain varieties with the same allele of Wx have different ECQs, implying that any other QTLs effect on ECQs. Because the effects of minor QTLs might be covered by major QTL such as Wx, many populations derived from bi-parental with similar AC values or the same Wx background have been developed to detect QTLs for starch RVA and eliminate the Wx effects [21,22,24,25]. The heredity of starch RVA pro le characters is very complex and affected by environmental factors [17,26].…”

Section: Introductionmentioning

confidence: 99%

QTL Mapping for the Starch Paste Viscosity of Rice (Oryza Sativa L.) Using a Chromosome Segment Substitution Lines Derived From Two Sequenced Cultivars With Same Wx Allele

Zhao

Zhou³

et al. 2021

Preprint

View full text Add to dashboard Cite

BackgroundEating and cooking qualities (ECQs) of rice (Oryza sativa L.) is one of the most important economic characters which affecting production and market value. The starch viscosity profile tested by Rapid visco analyzer (RVA) is the direct measure of ECQs that represents the changes in viscosity associated with starch gelatinization. RVA profiles of rice are controlled by a complex genetic system and affected by environment. It is necessary to identify genetic factors controlled the RVA profile characters for development of rice varieties with excellent ECQs. Although it is known that Waxy (Wx) is the major gene control the amylose content (AC) and ECQs, there still have other unknown genetic factors effecting on ECQs.ResultsQuantitative trait loci (QTL) for starch paste viscosity of rice was analyzed using chromosome segment substitution lines (CSSLs) developed from 9311 and Nipponbare with same Wx-b background. With this CSSLs, the effect of major locus Wx could be eliminated and the other locus associated with RVA profile could be identified. QTLs for seven traits of starch RVA profile were tested over 4 years in Nanjing, China. 310 QTLs were identified (from 1 to 55 QTLs for each trait). Among 136 repeated QTLs, 6 QTLs were stable and detected every year. In total of 26 marker intervals detected over 3 years or more, 13 showed pleiotropy with respect to controlling 2 to 6 starch RVA profile properties simultaneously. The stable QTL clusters which we mapped here were overlapped to some of the known starch synthesis–related genes (SSRGs). ConclusionsWithout the effect of major locus Wx, many QTLs associated with RVA profile of rice were identified and some of them were stable. Our study illustrated that the hereditary of rice starch RVA profile is complicated, pleiotropic effects and QTL hot spots are the key factors affecting starch RVA traits.

show abstract

Mapping quantitative trait loci associated with starch paste viscosity in rice (Oryza sativa L.) under different environmental conditions

Cited by 11 publications

References 51 publications

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

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

Understanding the genetics and chemistry of important quality traits in rice (Oryza sativa L.)

QTL Mapping for the Starch Paste Viscosity of Rice (Oryza Sativa L.) Using a Chromosome Segment Substitution Lines Derived From Two Sequenced Cultivars With Same Wx Allele

Contact Info

Product

Resources

About