A Comparison on Some Interval Mapping Approaches for QTL Detection

Akond, Zobaer; Alam, Jahangir; Hasan, Mohammad Nazmol; Uddin, Shalim; Alam, Munirul; Mollah, Md. Nurul Haque

doi:10.6026/97320630015090

Cited by 13 publications

(8 citation statements)

References 14 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Several consistent minor-effect QTLs were also identified for amylose content, with the most significant QTL located on chromosome 8. QTLs are considered significant when above the threshold LOD score 3.0 [43]. Other research reported two QTLs on chromosomes 1 (markers RM8111-RM14323, LOD 2.03) and 9 (markers RM219-RM23914, LOD 2.88) for amylose content [44], as well three QTLs on chromosomes 8 (RM506-RM1235, LOD 2.57), 9 (RM219-RM23914, LOD 2.66) and 10 (RM24934-RM25128, LOD 6.13) for protein content in 120 doubled haploid (DH) rice population.…”

Section: Plos Onementioning

confidence: 99%

Mapping QTLs underpin nutrition components in aromatic rice germplasm

et al. 2020

View full text Add to dashboard Cite

As rice is an important staple food globally, research for development and enhancement of its nutritional value it is an imperative task. Identification of nutrient enriched rice germplasm and exploiting them for breeding programme is the easiest way to develop better quality rice. In this study, we analyzed 113 aromatic rice germplasm in order to identify quantitative trait loci (QTL) underpinning nutrition components and determined by measuring the normal frequency distribution for Fe, Zn, amylose, and protein content in those rice germplasm. Comparatively, the germplasm Radhuni pagal, Kalobakri, Thakurbhog (26.6 ppm) and Hatisail exhibited the highest mean values for Fe (16.9 ppm), Zn (34.1 ppm), amylose (26.6 ppm) and protein content (11.0 ppm), respectively. Moreover, a significant linear relationship (R 2 = 0.693) was observed between Fe and Zn contents. Cluster analysis based on Mahalanobis D 2 distances revealed four major clusters of 113 rice germplasm, with cluster III containing a maximum 37 germplasm and a maximum inter-cluster distance between clusters III and IV. The 45 polymorphic SSRs and four trait associations exhibited eight significant quantitative trait loci (QTL) located on eight different chromosomes using composite interval mapping (CIM). The highly significant QTL (variance 7.89%, LOD 2.02) for protein content (QTL.pro.1) was observed on chromosome 1 at 94.9cM position. Also, four QTLs for amylose content were observed with the highly significant QTL.amy.8 located on chromosome 8 exhibiting 7.2% variance with LOD 1.83. Only one QTL (QTL.Fe.9) for Fe content was located on chromosome 9 (LOD 1.24), and two (QTL.Zn.4 and QTL.Zn.5) for Zn on chromosome 4 (LOD 1.71) and 5 (LOD 1.18), respectively. Overall, germplasm from clusters III and IV might offer higher heterotic response with the identified QTLs playing a significant role in any rice biofortification breeding program and released with development of new varieties.

show abstract

Section: Plos Onementioning

confidence: 99%

Mapping QTLs underpin nutrition components in aromatic rice germplasm

et al. 2020

View full text Add to dashboard Cite

show abstract

“…The next step is to perform a statistical analysis of the genotype-phenotype data to identify QTLs. The most commonly used method for QTL mapping is linkage analysis, which compares the phenotypic data with the molecular markers to identify regions of the genome that are associated with the phenotypic variation ( Akond et al, 2019 ). Once the QTLs are identified, further fine-mapping can be done to narrow down the chromosomal region relevant to the trait variation ( Raihan et al, 2016b ).…”

Section: Phase Ii: Molecular and Advanced Plant Breeding Technologymentioning

confidence: 99%

Green revolution to genome revolution: driving better resilient crops against environmental instability

Chawla,

Poonia,

Samantara

et al. 2023

Front. Genet.

View full text Add to dashboard Cite

Crop improvement programmes began with traditional breeding practices since the inception of agriculture. Farmers and plant breeders continue to use these strategies for crop improvement due to their broad application in modifying crop genetic compositions. Nonetheless, conventional breeding has significant downsides in regard to effort and time. Crop productivity seems to be hitting a plateau as a consequence of environmental issues and the scarcity of agricultural land. Therefore, continuous pursuit of advancement in crop improvement is essential. Recent technical innovations have resulted in a revolutionary shift in the pattern of breeding methods, leaning further towards molecular approaches. Among the promising approaches, marker-assisted selection, QTL mapping, omics-assisted breeding, genome-wide association studies and genome editing have lately gained prominence. Several governments have progressively relaxed their restrictions relating to genome editing. The present review highlights the evolutionary and revolutionary approaches that have been utilized for crop improvement in a bid to produce climate-resilient crops observing the consequence of climate change. Additionally, it will contribute to the comprehension of plant breeding succession so far. Investing in advanced sequencing technologies and bioinformatics will deepen our understanding of genetic variations and their functional implications, contributing to breakthroughs in crop improvement and biodiversity conservation.

show abstract

“…The remaining markers were binned according to their segregation patterns. After binning, we grouped the markers using a logarithm of odds (LOD) threshold of 3.0 [54]. Linkage groups were assigned according to the genomic position of the SNP markers determined during SNP calling.…”

Section: Maps Constructionmentioning

confidence: 99%

Heat Stress Tolerant-QTL Identified Using Backcrossed Recombinant Inbred Lines Derived From Intra-specifically Diverse <em>Aegilops tauschii</em> Accessions

Ahmed,

Kamal,

Gorafi

et al. 2023

Preprint

View full text Add to dashboard Cite

In the face of climate change, bringing more useful alleles and genes from wild relatives of wheat is crucial to develop climate-resilience varieties. We used two populations of backcrossed recombinant inbred lines (BIL1 and BIL2), developed using two intra-specifically diverse Aegilops tauschii accessions from lineage 1 and lineage 2, respectively, and backcrossing to common wheat cultivar ‘Norin 61’. The study aimed to identify quantitative trait loci (QTL) associated with heat stress (HS) tolerance. The two BILs were evaluated under heat stress environments in Sudan for phenology, plant height (PH), grain yield (GY), biomass (BIO), harvest index (HI), and thousand kernel weight (TKW). Grain yield was significantly correlated with BIO and TKW under HS; therefore, stress tolerance index (STI) was calculated for these traits as well as for GY. A total of 16 heat tolerant lines were identified based on GY and STI-GY. The QTL analysis performed using inclusive composite interval mapping identified a total of 40 QTLs in BIL1 and 153 QTLs in BIL2 across all environments. We detected 39 QTLs associated with GY-STI, BIO-STI, and TKW-STI in both populations (14 in BIL1 and 25 in BIL2). The QTL associated with STI were detected on chromosomes 1A, 3A, 5A, 2B, 4B, and all the D-subgenomes. We found that QTL detected only under HS for GY on chromosome 5A, TKW on 3B and 5B, PH on 3B and 4B, and grain filling duration on 2B. The higher number of QTLs identified in BIL2 for heat stress tolerance suggests the importance of assessing the effects of intraspecific variation of Ae. tauschii in wheat breeding as it could modulate the heat stress responses/adaptation. Our study provides useful genetic resources for uncovering heat-tolerant QTLs for wheat improvement for heat stress environments.

show abstract

A Comparison on Some Interval Mapping Approaches for QTL Detection

Cited by 13 publications

References 14 publications

Mapping QTLs underpin nutrition components in aromatic rice germplasm

Mapping QTLs underpin nutrition components in aromatic rice germplasm

Green revolution to genome revolution: driving better resilient crops against environmental instability

Heat Stress Tolerant-QTL Identified Using Backcrossed Recombinant Inbred Lines Derived From Intra-specifically Diverse <em>Aegilops tauschii</em> Accessions

Contact Info

Product

Resources

About