**Bulked Segregant Analysis Coupled with Whole-Genome Sequencing (BSA-Seq) Mapping Identifies a Novel** *pi21* **Haplotype Conferring Basal Resistance to Rice Blast Disease**

**Tingmin Liang 1,2,**†**, Wenchao Chi 1,**†**, Likun Huang 3, Mengyu Qu 1, Shubiao Zhang 3, Zi-Qiang Chen 2, Zai-Jie Chen 2, Dagang Tian 2, Yijie Gui 2, Xiaofeng Chen 1, Zonghua Wang 1,4, Weiqi Tang 1,\* and Songbiao Chen 1,\***


Received: 6 December 2019; Accepted: 19 March 2020; Published: 21 March 2020

**Abstract:** Basal or partial resistance has been considered race-non-specific and broad-spectrum. Therefore, the identification of genes or quantitative trait loci (QTLs) conferring basal resistance and germplasm containing them is of significance in breeding crops with durable resistance. In this study, we performed a bulked segregant analysis coupled with whole-genome sequencing (BSA-seq) to identify QTLs controlling basal resistance to blast disease in an F2 population derived from two rice varieties, 02428 and LiXinGeng (LXG), which differ significantly in basal resistance to rice blast. Four candidate QTLs, *qBBR-4*, *qBBR-7*, *qBBR-8*, and *qBBR-11*, were mapped on chromosomes 4, 7, 8, and 11, respectively. Allelic and genotypic association analyses identified a novel haplotype of the durable blast resistance gene *pi21* carrying double deletions of 30 bp and 33 bp in 02428 (*pi21-2428*) as a candidate gene of *qBBR-4*. We further assessed haplotypes of *Pi21* in 325 rice accessions, and identified 11 haplotypes among the accessions, of which eight were novel types. While the resistant *pi21* gene was found only in *japonica* before, three Chinese *indica* varieties, ShuHui881, Yong4, and ZhengDa4Hao, were detected carrying the resistant *pi21-2428* allele. The *pi21-2428* allele and *pi21-2428*-containing rice germplasm, thus, provide valuable resources for breeding rice varieties, especially *indica* rice varieties, with durable resistance to blast disease. Our results also lay the foundation for further identification and functional characterization of the other three QTLs to better understand the molecular mechanisms underlying rice basal resistance to blast disease.

**Keywords:** rice; blast disease; partial resistance; *pi21*; haplotype
