Dissection of QTL linked to grain yield and identification of candidate genes involved in grain yield formation using comparative SNP sequences analysis

Farouk, Issame; Gaboun, Fatima; Kehel, Zakaria; Alsaleh, Ahmad; Belkadi, Bouchra; Elouafi, Ismahane; Motowaj, Jihan; Maltouf, Abdelkarim Filali; Nachit, M. M.

doi:10.1109/iraset48871.2020.9091989

Cited by 1 publication

(3 citation statements)

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“…The genetic population used in this study (Lahn/Cham1) was published in [8,30] and presented in the conference [31]. The population was phenotyped for grain yield in 11 contrasting environments (cold / drought / heat).…”

Section: Plant Materialsmentioning

confidence: 99%

“…The Lahn/Cham1 genetic map that consisted of 1425 SNPs, 216 SSR and 31 other molecular markers was constructed using IciMapping program v 4.1.0.0 was presented in [31].…”

Section: Plant Materialsmentioning

confidence: 99%

“…More informations about the environments, DNA sequences size, environmental conditions, QTL intervals and flanking markers are summarized in Table 1. Thereafter, the sequences isolated were served as queries for Blast search in NCBI against Rice and Brachypodium genomes to identify the candidate genes composing these QTLs detected in the four environments (EP, INC, RF, and RQ), see Figure 1 In multi-environmental analysis, the 583 SNPs selected from the QTLs regions and harbored by durum chromosomes [31] were analyzed through Blast (Basic Local Alignment Search Tool) search homology using the URGI Blast of (INRA), France (https://urgi.versailles.inra.fr/blast/blast.php) with the aim to expand the SNP sequences in terms of length [34] (Figure 2). Subsequently, the derived genomic sequences (280bp) were served as query to identify the candidate genes using Blast search homology in NCBI (National Center for Biotechnology Information, the USA), see Figure 2.…”

Section: Snps Annotation and Candidate Genes Identificationmentioning

confidence: 99%

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Dissection of Quantitative Trait Loci (QTL), annotation of Single Nucleotide Polymorphism (SNP), and Identification of Candidate Genes for Grain Yield in Triticum turgidum L. var durum

Farouk¹,

Alsaleh²,

Motowaj³

et al. 2020

Adv. sci. technol. eng. syst. j.

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Durum wheat (Triticum turgidum L. var durum) is among the most important crops in the world. High and stable grain yield in diverse environments is the major objective in durum breeding programs. This trait is linked to the quantitative trait loci (QTL). For the detection of QTL linked to the grain yield, it is necessary to construct a high-density genetic linkage map. The aims of this study were to detect the candidate genes comprised in the QTLs on 2A chromosome linked to grain yield and annotate the single nucleotide polymorphisms (SNPs). The linkage map of Lahn/Cham1 population was used to identify QTLs. In multienvironmental analysis and employing bioinformatic approaches, 583 sequences corresponding to the SNPs markers selected from the detected QTL regions were analyzed, 122 SNP sequences were annotated of which 53% of the candidate genes were involved in stresses tolerance, 29.5% in plant development and growth, and 3.3% in cell transport. Moreover, 1.6% of candidate genes were retrotransposon and transposon 2.4% with unknown function. Further 9.8% were related in other cellular processes. The results also showed that 66.7% of the candidate genes harbored on 4B chromosome, were involved in stresses tolerance and 33.3% in plant development and growth. Additionally, in the specific and stressed environments analysis, the DNA sequences of the four QTL detected on 2A chromosome were used for homology search, 546 candidate genes were identified of which some were present in several QTL (F-box gene family, hydroxyproline-rich glycoproteinlike), retrotransposons and transposons and others. This study provided information on employing SNPs markers to detect candidate genes linked with grain yield trait in durum wheat in contrasting environments (dry, cold, hot).

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Section: Plant Materialsmentioning

confidence: 99%

“…The Lahn/Cham1 genetic map that consisted of 1425 SNPs, 216 SSR and 31 other molecular markers was constructed using IciMapping program v 4.1.0.0 was presented in [31].…”

Section: Plant Materialsmentioning

confidence: 99%