Detection of consensus genomic regions associated with root architecture of bread wheat on groups 2 and 3 chromosomes using QTL meta–analysis

Darzi-Ramandi, Hadi; Shariati, Vahid; Tavakol, Elahe; Najafi-Zarini, Hamid; Bilgrami, Sayedeh Saba; Razavi, Khadijeh

doi:10.21475/ajcs.17.11.07.pne312

Cited by 22 publications

(18 citation statements)

References 49 publications

(44 reference statements)

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“…Previous studies reporting MQTLs for root traits have been carried out by Darzi-Ramandi 6 and Iannucci 19 . From an initial database comprising 243 QTLs reported from 12 different experiments, Darzi-Ramandi 6 used for meta-analysis only 53 QTLs located on chromosome groups 2 and 3, as they carried most of the QTLs for root traits. After meta-analysis, these authors grouped the QTLs into 8 MQTLs.…”

Section: Discussionmentioning

confidence: 99%

“…Modelling studies conducted in Australia have shown that direct selection for deeper, more effective roots could considerably increase the capture of water and nitrogen from soil, thus resulting in a wheat yield improvement under rainfed conditions 4,5 . However, because of the inherent difficulties in measuring and assessing it, root system architecture has not been considered a selection trait in the breeding process 6 . Discovering quantitative trait loci (QTLs) controlling root architecture and identifying molecular markers linked to them are an essential tool for exploiting root traits in breeding programmes through marker-assisted selection.…”

Section: Introductionmentioning

confidence: 99%

“…QTL meta-analysis for root-related traits was performed previously by Darzi-Ramandi et al . 6 , who only considered 53 QTLs from chromosome groups 2 and 3 for the analysis, and by Iannucci et al . 19 , who performed the analysis in durum wheat using 100 QTLs retrieved from the literature together with 17 QTLs discovered in their study.…”

Section: Introductionmentioning

confidence: 99%

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Discovering consensus genomic regions in wheat for root-related traits by QTL meta-analysis

Soriano

Álvaro

2019

Sci Rep

107

123

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Root system architecture is crucial for wheat adaptation to drought stress, but phenotyping for root traits in breeding programmes is difficult and time-consuming owing to the belowground characteristics of the system. Identifying quantitative trait loci (QTLs) and linked molecular markers and using marker-assisted selection is an efficient way to increase selection efficiency and boost genetic gains in breeding programmes. Hundreds of QTLs have been identified for different root traits in the last few years. In the current study, consensus QTL regions were identified through QTL meta-analysis. First, a consensus map comprising 7352 markers was constructed. For the meta-analysis, 754 QTLs were retrieved from the literature and 634 of them were projected onto the consensus map. Meta-analysis grouped 557 QTLs in 94 consensus QTL regions, or meta-QTLs (MQTLs), and 18 QTLs remained as singletons. The recently published genome sequence of wheat was used to search for gene models within the MQTL peaks. As a result, gene models for 68 of the 94 Root_MQTLs were found, 35 of them related to root architecture and/or drought stress response. This work will facilitate QTL cloning and pyramiding to develop new cultivars with specific root architecture for coping with environmental constraints.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Discovering consensus genomic regions in wheat for root-related traits by QTL meta-analysis

Soriano

Álvaro

2019

Sci Rep

107

123

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“…Reducing the CI of the MQTLs in comparison with QTLs is another indispensable perks of MQTL analysis 11 – 15 . More recently, a number of studies have applied the QTL meta-analysis method to different traits in wheat, including root morphological traits 13 , 16 , grain traits 11 , fusarium head blight resistance 14 , 17 , adaptation to drought and heat stress 18 and leaf rust resistance 19 .…”

Section: Introductionmentioning

confidence: 99%

Detection of genomic regions associated with tiller number in Iranian bread wheat under different water regimes using genome-wide association study

Bilgrami

Ramandi

Shariati

et al. 2020

Sci Rep

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Two of the important traits for wheat yield are tiller and fertile tiller number, both of which have been thought to increase cereal yield in favorable and unfavorable environments. A total of 6,349 single nucleotide polymorphism (SNP) markers from the 15 K wheat Infinium array were employed for genome-wide association study (GWAS) of tillering number traits, generating a physical distance of 14,041.6 Mb based on the IWGSC wheat genome sequence. GWAS analysis using Fixed and random model Circulating Probability Unification (FarmCPU) identified a total of 47 significant marker-trait associations (MTAs) for total tiller number (TTN) and fertile tiller number (FTN) in Iranian bread wheat under different water regimes. After applying a 5% false discovery rate (FDR) threshold, a total of 13 and 11 MTAs distributed on 10 chromosomes were found to be significantly associated with TTN and FTN, respectively. Linked single nucleotide polymorphisms for IWB39005 (2A) and IWB44377 (7A) were highly significantly associated (FDR < 0.01) with TTN and FTN traits. Moreover, to validate GWAS results, meta-analysis was performed and 30 meta-QTL regions were identified on 11 chromosomes. The integration of GWAS and meta-QTLs revealed that tillering trait in wheat is a complex trait which is conditioned by the combined effects of minor changes in multiple genes. The information provided by this study can enrich the currently available candidate genes and genetic resources pools, offering evidence for subsequent analysis of genetic adaptation of wheat to different climatic conditions of Iran and other countries. Bread wheat (Triticum aestivum L., genomes AABBDD, 2n = 6x = 42), is a major cereal crop, supplying 20% of the total energy and protein of the world's diet 1. Its production and productivity, especially in arid and semiarid regions such as Iran, are considerably constrained by extreme drought and heat stresses. Breeding for grain yield is the final step to produce stress-tolerant crop plants, since grain yield is a complex trait with low heritability, which is controlled by multiple genes and is affected by a lot of environmental factors, other traits such as yield components can be employed to overcome the limitations. Tillering is a crucial factor for wheat yield because of its involvement in grain weight and grain number determination. Moreover, it is a determinant of grain yield,

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“…During recent years, meta-analysis approach has become a mainstream practice for integrating the QTL information data obtained from multiple independent mapping experiments and identification of most consistent meta-QTLs (MQTLs) across diverse environments. This approach has been applied in several economically important food crops, including maize, wheat, barley and rice (Martinez et al 2016;Darzi-Ramandi et al 2017;Khahani et al 2019;Raza et al 2019). These studies provided a proof of concept for identification and prioritization of trait linked MQTLs/candidate genes and offered new biological data for the development of stress tolerant rice cultivars.…”

Section: Introductionmentioning

confidence: 99%

Reproductive tissues-specific meta-QTLs and candidate genes for development of heat-tolerant rice cultivars

Raza

Riaz

Sabar

2020

Preprint

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Rice holds the key to future food security. In rice-growing areas, temperature has already reached an optimum level for growth, hence, any further increase due to global climate change could significantly reduce rice yield. Several mapping studies have identified a plethora of reproductive tissue-specific and heat stress associated inconsistent quantitative trait loci (QTL), which could be exploited for improvement of heat tolerance. In this study, we performed a meta-analysis on previously reported QTLs and identified 35 most consistent meta-QTLs (MQTLs) across diverse genetic backgrounds and environments. Genetic and physical intervals of nearly 66% MQTLs were narrower than 5 cM and 2 Mb respectively, indicating hotspot genomic regions for heat tolerance. Comparative analyses of MQTLs underlying genes with microarray and RNA-seq based transcriptomic data sets revealed a core set of 45 heat-responsive genes, among which 24 were reproductive tissue-specific and have not been studied in detail before. Remarkably, all these genes corresponded to various stress associated functions, ranging from abiotic stress sensing to regulating plant stress responses, and included heat-shock genes (OsBiP2, OsMed37_1), transcription factors (OsNAS3, OsTEF1, OsWRKY10, OsWRKY21), transmembrane transporters (OsAAP7A, OsAMT2;1), sugar metabolizing (OsSUS4, α -Gal III) and abiotic stress (OsRCI2-7, SRWD1) genes. Functional data evidences from Arabidopsis heat-shock genes also suggest that OsBIP2 may be associated with thermotolerance of pollen tubes under heat stress conditions. Furthermore, promoters of identified genes were enriched with heat, dehydration, pollen and sugar responsive cis-acting regulatory elements, proposing a common regulatory mechanism might exist in rice for mitigating reproductive stage heat stress. These findings strongly support our results and provide new candidate genes for fast-track development of heat-tolerant rice cultivars. Key MessageBy integrating genetics and genomics data, reproductive tissues-specific and heat stress responsive 35 meta-QTLs and 45 candidate genes were identified, which could be exploited through marker-assisted breeding for fast-track development of heat-tolerant rice cultivars.

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Detection of consensus genomic regions associated with root architecture of bread wheat on groups 2 and 3 chromosomes using QTL meta–analysis

Cited by 22 publications

References 49 publications

Discovering consensus genomic regions in wheat for root-related traits by QTL meta-analysis

Discovering consensus genomic regions in wheat for root-related traits by QTL meta-analysis

Detection of genomic regions associated with tiller number in Iranian bread wheat under different water regimes using genome-wide association study

Reproductive tissues-specific meta-QTLs and candidate genes for development of heat-tolerant rice cultivars

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