NAM-BSA: A Bulked Segregant Analysis Method Using a NAM Population

Area of Science:

• Plant genetics and genomics
• Quantitative trait loci (QTL) mapping
• Crop improvement

Background:

• Quantitative trait loci (QTL) mapping, including BSA-seq (QTL-seq) and GWAS, are key genetic mapping approaches.
• BSA-seq offers a cost-effective and efficient method for QTL mapping.
• Tailored BSA methodologies are crucial for diverse species and genetic architectures.

Purpose of the Study:

• To construct a nested association mapping (NAM) population in rice using wild rice donors and an elite cultivated variety.
• To identify candidate genes and genomic regions associated with plant height using BSA-seq.
• To evaluate the potential of NAM-BSA technology for dissecting complex traits in rice.

Main Methods:

• Construction of a BC4F8 population from six wild rice (Oryza rufipogon) introgression lines and cultivated rice Youzhan 8 (YZ8).
• Genotyping of 1819 NAM population lines for the Sd1 gene and phenotypic assessment of plant height.
• Bulked Segregant Analysis sequencing (BSA-seq) on selected high-plant-height (HP) and low-plant-height (LP) bulks, followed by RNA-seq and RT-qPCR validation.

Main Results:

• A significant association between the 383 bp deletion in the Sd1 gene and low plant height (LP) phenotype was observed.
• BSA-seq identified 33 significantly associated candidate intervals, including the known plant height gene D18 on chromosome 1.
• Two major candidate genomic regions on chromosome 8 (4.60-5.76 Mb and 7.29-7.33 Mb) and two key candidate genes (LOC_Os08g09900, LOC_Os08g09000) were identified.

Conclusions:

• The NAM-BSA technology is effective for detecting QTL associated with complex traits like plant height in rice.
• This study provides a novel technical strategy for the genetic dissection of complex traits in rice.
• Identified candidate genes require further functional characterization to confirm their role in plant height regulation.