Genetic Mapping by Sequencing More Precisely Detects Loci Responsible for Anaerobic Germination Tolerance in Rice

• Main Authors: John Carlos I. Ignacio, Maricris Zaidem, Carlos Casal, Shalabh Dixit, Tobias Kretzschmar, Jaime M. Samaniego, Merlyn S. Mendioro, Detlef Weigel, Endang M. Septiningsih
• Format: Article
• Language: English
• Published: MDPI AG 2021-04-01
• Series: Plants
• Subjects: quantitative trait locus (QTL); sequencing based genotyping; RAD-seq; anaerobic germination (AG); rice (<i>Oryza sativa</i>)
• Online Access: https://www.mdpi.com/2223-7747/10/4/705

Direct seeded rice (DSR) is a mainstay for planting rice in the Americas, and it is rapidly becoming more popular in Asia. It is essential to develop rice varieties that are suitable for this type of production system. ASD1, a landrace from India, possesses several traits desirable for direct-seeded fields, including tolerance to anaerobic germination (AG). To map the genetic basis of its tolerance, we examined a population of 200 F_2:3 families derived from a cross between IR64 and ASD1 using the restriction site-associated DNA sequencing (RAD-seq) technology. This genotyping platform enabled the identification of 1921 single nucleotide polymorphism (SNP) markers to construct a high-resolution genetic linkage map with an average interval of 0.9 cM. Two significant quantitative trait loci (QTLs) were detected on chromosomes 7 and 9, <i>qAG7</i> and <i>qAG9</i>, with LOD scores of 7.1 and 15.0 and R² values of 15.1 and 29.4, respectively. Here, we obtained more precise locations of the QTLs than traditional simple sequence repeat and low-density SNP genotyping methods and may help further dissect the genetic factors of these QTLs.