Browse
Submit Data
Databases
API
Help

Dataset Information

29 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Detecting CSSLs and yield QTLs with additive, epistatic and QTL×environment interaction effects from Oryza sativa × O. nivara IRGC81832 cross.

ABSTRACT: Chromosome segment substitution lines (CSSLs) are useful tools for precise mapping of quantitative trait loci (QTLs) and the evaluation of gene action and interaction in inter-specific crosses. In this study, a set of 90 back cross lines at BC₂F₈ generation derived from Swarna x Oryza nivara IRGC81832 was evaluated for yield traits under irrigated conditions in wet seasons of 3 consecutive years. We identified a set of 70 chromosome segment substitution lines, using genotyping data from 140 SSR markers covering 94.4% of O. nivara genome. Among these, 23 CSSLs were significantly different for 7 traits. 22 QTLs were detected for 11 traits with 6.51 to 46.77% phenotypic variation in 90 BILs. Three pleiotropic genomic regions associated with yield traits were mapped on chromosomes 1, 8 and 11. The marker interval RM206-RM144 at chromosome 11 was recurrently detected for various yield traits. Ten QTLs were identified consistently in the three consecutive years of testing. Seventeen pairs of significant epistatic QTLs (E-QTLs) were detected for days to flowering, days to maturity and plant height. Chromosome segments from O. nivara contributed trait enhancing alleles. The significantly improved lines and the stable QTLs identified in this study are valuable resource for gene discovery and yield improvement.

SUBMITTER: Balakrishnan D

PROVIDER: S-EPMC7210974 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Identification of Major Effect QTLs for Agronomic Traits and CSSLs in Rice from Swarna/Oryza nivara Derived Backcross Inbred Lines.

Project description:Backcross inbred lines (BILs) derived from elite x wild crosses are very useful for basic studies and breeding. The aim of this study was to map quantitative trait loci (QTLs) associated with yield and related traits and to identify chromosomal segment substitution lines (CSSLs) from unselected BC2F8 BILs of Swarna/Oryza nivara IRGC81848. In all, 94 BILs were field evaluated in 2 years (wet seasons, 2014 and 2015) for nine traits; days to 50% flowering, days to maturity (DM), plant height (PH), number of tillers, number of productive tillers, panicle weight, yield per plant, bulk yield, and biomass. BILs were genotyped using 111 polymorphic simple sequence repeats distributed across the genome. Fifteen QTLs including 10 novel QTLs were identified using composite interval mapping, Inclusive composite interval mapping and multiple interval mapping (MIM). O. nivara alleles were trait-enhancing in 26% of QTLs. Only 3 of 15 QTLs were also reported previously in BC2F2 of the same cross. These three included the two major effect QTLs for DM and PH detected in both years with 13 and 20% phenotypic variance. Further, a set of 74 CSSLs was identified using CSSL Finder and 22 of these showed significantly higher values than Swarna for five yield traits. CSSLs, 220S for panicle weight and 10-2S with consistent high yield in both years are worthy of large scale field evaluation. The major QTLs and 22 significantly different CSSLs are a useful resource for rice improvement and dissecting yield related traits.

| S-EPMC5480306 | biostudies-literature

Genotype × Environment Interactions of Yield Traits in Backcross Introgression Lines Derived from Oryza sativa cv. Swarna/Oryza nivara.

Project description:Advanced backcross introgression lines (BILs) developed from crosses of Oryza sativa var. Swarna/O. nivara accessions were grown and evaluated for yield and related traits. Trials were conducted for consecutive three seasons in field conditions in a randomized complete block design with three replications. Data on yield traits under irrigated conditions were analyzed using the Additive Main Effect and Multiplicative Interaction (AMMI), Genotype and Genotype × Environment Interaction (GGE) and modified rank-sum statistic (YSi) for yield stability. BILs viz., G3 (14S) and G6 (166S) showed yield stability across the seasons along with high mean yield performance. G3 is early in flowering with high yield and has good grain quality and medium height, hence could be recommended for most of the irrigated locations. G6 is a late duration genotype, with strong culm strength, high grain number and panicle weight. G6 has higher yield and stability than Swarna but has Swarna grain type. Among the varieties tested DRRDhan 40 and recurrent parent Swarna showed stability for yield traits across the seasons. The component traits thousand grain weight, panicle weight, panicle length, grain number and plant height explained highest genotypic percentage over environment and interaction factors and can be prioritized to dissect stable QTLs/ genes. These lines were genotyped using microsatellite markers covering the entire rice genome and also using a set of markers linked to previously reported yield QTLs. It was observed that wild derived lines with more than 70% of recurrent parent genome were stable and showed enhanced yield levels compared to genotypes with higher donor genome introgressions.

| S-EPMC5070172 | biostudies-literature

Fine mapping of stable QTLs related to eating quality in rice (Oryza sativa L.) by CSSLs harboring small target chromosomal segments.

Project description:Amylose content (AC) and viscosity profile are primary indices for evaluating eating and cooking qualities of rice grain. Using chromosome segment substitution lines (CSSLs), previous studies identified a QTL cluster of genes for rice eating and cooking quality in the interval R727-G1149 on chromosome 8. In this study we report two QTLs for viscosity parameters, respectively controlling setback viscosity (SBV) and consistency viscosity (CSV), located in the same interval using rapid viscosity analyzer (RVA) profile as an indicator of eating quality. Previously reported QTL for AC was dissected into two components with opposite genetic effects. Of four QTLs, qCSV-8 and qAC-8-2 had stable genetic effects across three and four environments, respectively. qSBV-8, qCSV-8 and qAC-8-1 partly overlapped, but were separated from qAC-8-2. Based on data from an Affymetrix rice GeneChip, two genes related to starch biosynthesis at the qAC-8-2 locus were chosen for further quantitative expression analysis. Both genes showed enhanced expression in sub-CSSLs carrying the target qAC-8-2 allele, but not in sub-CSSLs without the target qAC-8-2 allele, indicating their possible role in rice quality determination. Molecular markers closely linked to the two stable QTL provide the opportunity for marker-assisted selection (MAS) in breeding high quality rice.

| S-EPMC3406775 | biostudies-literature

Epistatic QTLs for yield heterosis in tomato.

Project description:Controlled population development and genome-wide association studies have proven powerful in uncovering genes and alleles underlying complex traits. An underexplored dimension of such studies is the phenotypic contribution of nonadditive interactions between quantitative trait loci (QTLs). Capturing of such epistasis in a genome-wide manner requires very large populations to represent replicated combinations of loci whose interactions determine phenotypic outcomes. Here, we dissect epistasis using a densely genotyped population of 1,400 backcross inbred lines (BILs) between a modern processing tomato inbred (Solanum lycopersicum) and the Lost Accession (LA5240) of a distant, green-fruited, drought-tolerant wild species, Solanum pennellii. The homozygous BILs, each harboring an average of 11 introgressions and their hybrids with the recurrent parents, were phenotyped for tomato yield components. Population-wide mean yield of the BILs was less than 50% of that of their hybrids (BILHs). All the homozygous introgressions across the genome reduced yield relative to recurrent parent, while several QTLs of the BILHs independently improved productivity. Analysis of two QTL scans showed 61 cases of less-than-additive interactions and 19 cases of more-than-additive interactions. Strikingly, a single epistatic interaction involving S. pennellii QTLs on chromosomes 1 and 7, that independently did not affect yield, increased fruit yield by 20 to 50% in the double introgression hybrid grown in irrigated and dry fields over a period of 4 y. Our work demonstrates the power of large, interspecific controlled population development to uncover hidden QTL phenotypes and how rare epistatic interactions can improve crop productivity via heterosis.

| S-EPMC10083602 | biostudies-literature

Genomic structure analysis of a set of Oryza nivara introgression lines and identification of yield-associated QTLs using whole-genome resequencing.

Project description:Oryza nivara, an annual wild AA-genome species of rice, is an important gene pool for broadening the genetic diversity of cultivated rice (O. sativa L.). Towards identifying and utilizing favourable alleles from O. nivara, we developed a set of introgression lines (ILs) by introducing O. nivara segments into the elite indica rice variety 93-11 background through advanced backcrossing and repeated selfing. Using whole-genome resequencing, a high-density genetic map containing 1,070 bin-markers was constructed for the 131 ILs, with an average length of 349?kb per bin. The 131 ILs cover 95% of O. nivara genome, providing a relatively complete genomic library for introgressing O. nivara alleles for trait improvement. Using this high-density bin-map, QTL mapping for 13 yield-related traits was performed and a total of 65 QTLs were detected across two environments. At ~36.9% of detected QTLs, the alleles from O. nivara conferred improving effects on yield-associated traits. Six cloned genes, Sh4/SHA1, Bh4, Sd1, TE/TAD1, GS3 and FZP, colocalised in the peak intervals of 9 QTLs. In conclusion, we developed new genetic materials for exploration and use of beneficial alleles from wild rice and provided a basis for future fine mapping and cloning of the favourable O. nivara-derived QTLs.

| S-EPMC4890301 | biostudies-literature

Yield-enhancing heterotic QTL transferred from wild species to cultivated rice Oryza sativa L.

Project description:Utilization of "hidden genes" from wild species has emerged as a novel option for enrichment of genetic diversity for productivity traits. In rice we have generated more than 2000 lines having introgression from 'A' genome-donor wild species of rice in the genetic background of popular varieties PR114 and Pusa44 were developed. Out of these, based on agronomic acceptability, 318 lines were used for developing rice hybrids to assess the effect of introgressions in heterozygous state. These introgression lines and their recurrent parents, possessing fertility restoration ability for wild abortive (WA) cytoplasm, were crossed with cytoplasmic male sterile (CMS) line PMS17A to develop hybrids. Hybrids developed from recurrent parents were used as checks to compare the performance of 318 hybrids developed by hybridizing alien introgression lines with PMS17A. Seventeen hybrids expressed a significant increase in yield and its component traits over check hybrids. These 17 hybrids were re-evaluated in large-size replicated plots. Of these, four hybrids, viz., ILH299, ILH326, ILH867 and ILH901, having introgressions from O. rufipogon and two hybrids (ILH921 and ILH951) having introgressions from O. nivara showed significant heterosis over parental introgression line, recurrent parents and check hybrids for grain yield-related traits. Alien introgressions were detected in the lines taken as male parents for developing six superior hybrids, using a set of 100 polymorphic simple sequence repeat (SSR) markers. Percent introgression showed a range of 2.24 from in O. nivara to 7.66 from O. rufipogon. The introgressed regions and their putative association with yield components in hybrids is reported and discussed.

| S-EPMC4064972 | biostudies-literature

Identifying QTLs for Grain Size in a Colossal Grain Rice (Oryza sativa L.) Line, and Analysis of Additive Effects of QTLs.

Project description:Grain size is an important component of quality and harvest traits in the field of rice breeding. Although numerous quantitative trait loci (QTLs) of grain size in rice have been reported, the molecular mechanisms of these QTLs remain poorly understood, and further research on QTL observation and candidate gene identification is warranted. In our research, we developed a suite of F2 intercross populations from a cross of 9311 and CG. These primary populations were used to map QTLs conferring grain size, evaluated across three environments, and then subjected to bulked-segregant analysis-seq (BSA-seq). In total, 4, 11, 12 and 14 QTLs for grain length (GL), grain width (GW), 1000-grain weight (TGW), and length/width ratio (LWR), respectively, were detected on the basis of a single-environment analysis. In particular, over 200 splicing-related sites were identified by whole-genome sequencing, including one splicing-site mutation with G>A at the beginning of intron 4 on Os03g0841800 (qGL3.3), producing a smaller open reading frame, without the third and fourth exons. A previous study revealed that the loss-of-function allele caused by this splicing site can negatively regulate rice grain length. Furthermore, qTGW2.1 and qGW2.3 were new QTLs for grain width. We used the near-isogenic lines (NILs) of these GW QTLs to study their genetic effects on individuals and pyramiding, and found that they have additive effects on GW. In summary, these discoveries provide a valuable genetic resource, which will facilitate further study of the genetic polymorphism of new rice varieties in rice breeding.

| S-EPMC8998697 | biostudies-literature

Screening germplasm and detecting QTLs for mesocotyl elongation trait in rice (Oryza sativa L.) by association mapping.

Project description:BackgroundRice is one of the most important food crops in the world and mainly cultivated in paddy field by transplanting seedlings. However, increasing water scarcity due to climate change, labor cost for transplanting, and competition from urbanization is making this traditional method of rice production unsustainable in the long term. In the present study, we mined favorable alleles for mesocotyl elongation length (MEL) by combining the phenotypic data of 543 rice accessions with genotypic data of 262 SSR markers through association mapping method.ResultsAmong the 543 rice accessions studied, we found 130 accessions could elongate mesocotyl length under dark germination condition. A marker-trait association analysis based on a mixed linear model revealed eleven SSR markers were associated with MEL trait with p-value less than 0.01. Among the 11 association loci, seven were novel. In total, 30 favorable marker alleles for MEL were mined, and RM265-140 bp showed the highest phenotypic effect value of 1.8 cm with Yuedao46 as the carrier accession. The long MEL group of rice accessions had higher seedling emergence rate than the short MEL group in the field. The correlation coefficient (r GCC-FSC = 0.485**) between growth chamber condition (GCC) and field soil condition (FSC) showed positive relationship and highly significant (P < 0.01) indicating that the result obtained in GCC could basically represent that obtained under FSC.ConclusionNot every genotype of the rice possesses the ability to elongate its mesocotyl length under dark or deep sowing condition. Mesocotyl elongation length is a quantitative trait controlled by many gene loci, and can be improved by pyramiding favorable alleles dispersed at different loci in different germplasm into a single genotype.

| S-EPMC9930352 | biostudies-literature

Two Novel QTLs for the Harvest Index that Contribute to High-Yield Production in Rice (Oryza sativa L.).

Project description:BackgroundThe harvest index (HI) is a measure of the biological success of forming harvestable products. However, our understanding of the genetic basis of HI in rice (Oryza sativa L.) is limited, because it is a complex trait consisting of various yield-related traits and physiological attributes. YTH183 is a high-yielding line with large panicles and high HI derived from a cross between the Indica Group variety IR 64 and the NPT line IR 69093-41-2-3-2 (YP5).ResultsHere, we detected two novel QTLs for HI, designated qHI5.1 on chromosome 5 and qHI8.1 on chromosome 8, by using 155 recombinant inbred lines (RILs) derived from the cross between IR 64 and YTH183. The YTH183 allele at qHI5.1 contributed to a wide grain, resulting in heavy grain weight and panicle weight, and was consistently effective under the different environmental conditions of subtropical (Ishigaki) and temperate (Tsukuba) regions. Genetic polymorphism revealed that qHI5.1 was identical to GSE5/GW5, which is known to control the grain weight. On the other hand, although qHI8.1 functioned additively with qHI5.1 for higher HI, it did not show any significant effect on grain or panicle weight. In addition, its effects on HI were shown only in the first seasons at Ishigaki but not at Tsukuba or in the second season at Ishigaki.ConclusionOur results indicate that qHI5.1 controls the grain size, regardless of whether environmental conditions are of subtropical or temperate regions, while qHI8.1 might be involved in controlling the physiological processes of source ability or the translocation of photosynthesis products from vegetative organs to grains depending on environmental conditions during the maturing stage. These QTLs will be useful genetic resources for future breeding programs to break through the ceiling of maximum yield in Indica Group varieties.

| S-EPMC7876197 | biostudies-literature

QTL-seq identifies cooked grain elongation QTLs near soluble starch synthase and starch branching enzymes in rice (Oryza sativa L.).

Project description:Grain quality is one of the main targets that rice breeders focus on to improve elite rice varieties. Several characteristics are considered when determine rice grain quality, such as aroma, amylose content (AC), gelatinization temperature (GT) and, especially, lengthwise grain elongation (GE). GE is a desirable feature in premium rice of high quality, such as India and Pakistan' Basmati. Inheritance of GE in rice has not been clearly elucidated due to its complex and inconsistent pattern. In this study, we identified QTLs for GE in rice using bulk-segregant analysis (BSA) and whole-genome sequencing based on an F2 population segregated for GE as well as AC and GT. We identified two QTLs on chromosome 6, qGE6.1 and qGE6.2, and another QTL on chromosome 4, qGE4.1. qGE6.1 and qGE6.2 were located near starch synthase IIa (SSIIa) and starch branching enzyme III (SBEIII), respectively, and qGE4.1 was located near starch branching enzyme IIa (SBEIIa). qGE6.1 was considered to be the major QTL for GE based on this population, and SSIIa was suggested to be the best candidate gene associated with the GE trait. The results of this study may be useful for breeding rice with increased grain elongation and different starch properties.

| S-EPMC6554297 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data