Comparative Genomics Analysis of Core MQTL

The Rice Genome Annotation Project (RGAP) database (https://rice.uga.edu/cgi-bin/gbrowser/rice, accessed on 20, 4 2023) was used to retrieve the functional candidate genes at CI of core MQTL. The above database was then used to obtain the description of the CGs in the core MQTL intervals. To enhance the accuracy of our assumptions on CGs, the orthologous genes in the core MQTL regions were placed over the genomes of sorghum and maize. The TBtools software [42 (link)] was used to visualize the gene density and orthologue genes in sorghum and maize.

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Aloryi K.D., Okpala N.E., Guo H., Karikari B., Amo A., Bello S.F., Saini D.K., Akaba S, & Tian X. (2024). Integrated meta-analysis and transcriptomics pinpoint genomic loci and novel candidate genes associated with submergence tolerance in rice. BMC Genomics, 25, 338.

Publication 2024

Corresponding Organization :

Other organizations : Yangtze University, University of Chinese Academy of Sciences, Université Laval, Texas A&M University, South China Agricultural University, Punjab Agricultural University, University of Cape Coast

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Variable analysis

independent variables

Retrieval of functional candidate genes at CI of core MQTL from the Rice Genome Annotation Project (RGAP) database
Obtaining the description of the CGs in the core MQTL intervals from the RGAP database
Placing the orthologous genes in the core MQTL regions over the genomes of sorghum and maize
Using the TBtools software to visualize the gene density and orthologue genes in sorghum and maize

dependent variables

Not explicitly mentioned

control variables

Not explicitly mentioned

controls

No positive or negative controls were explicitly mentioned in the provided information.

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