Identification of two QTLs, BPH41 and BPH42, and their respective gene candidates for brown planthopper resistance in rice

Abstract

The brown planthopper (BPH) is the leading cause of insect damage to rice plants and BPH infestations have caused profound losses in rice production since the 1970’s. There is an urgent need to discover new BPH resistance genes to ensure the successful production of rice. Here, a new BPH resistance source provided by SeedWorks International Pvt. Ltd., SWD10, was used for this purpose. QTL mapping using 232 F2 progenies and 216 polymorphic markers revealed two dominant BPH resistance QTLs, BPH41 and BPH42, located on chromosome 4. BPH resistance mechanism test revealed that antibiosis and antixenosis mechanisms both play a role in BPH resistance conferred by these two QTLs. The QTLs were delimited between markers SWRm_01617 and SWRm_01522 for BPH41, and SWRm_01695 and SWRm_00328 for BPH42. Additionally, using RNA-seq data of lines containing the resistant QTLs, we shortlisted four and three gene candidates for BPH41 and BPH42, respectively. Differential gene expression analysis of lines containing the QTLs suggested that SWD10 BPH resistance is contributed by the plant’s innate immunity and the candidate genes may be part of the rice innate immunity pathway. Currently, the newly identified QTLs are being utilized for breeding BPH resistant rice varieties and hybrids.

Recent Advances in Molecular Mechanism and Breeding Utilization of Brown Planthopper Resistance Genes in Rice: An Integrated Review

“…For example, Yang et al (2019) [65] have positioned Bph37 between RM302 and YM35 in chromosome 1 in IR64, while Zhou et al (2021) [66] has cloned a resistance gene on chromosome 6 in SE382 and also named it Bph37. Similarly, Tan et al (2022) [69] have located the resistance gene Bph41 between SWRm_01617 and SWRm_01522 in chromosome 4, and in the same year, Wang et al (2022) [70] have reported Bph41, locating it between the molecular markers W4-4-3 and W1-6-3 on chromosome 4. As a result, the nomenclature of BPH-resistant genes has become confusing.…”

Recent Advances in the Genetic and Biochemical Mechanisms of Rice Resistance to Brown Planthoppers (Nilaparvata lugens Stål)

“…Three genes (bph11, qBph3, and Bph14) were clustered between 35.60 and 35.80 Mb of chromosome 3L [29,32,34]. A total of 21 genes were located on chromosome 4: five genes (Bph44(t), qBph4.3, Bph33, Bph30, and Bph41) were clustered between 0.17 and 1.10 Mb on chromosome 4S [2,24,[35][36][37]; 11 genes (Bph40, Bph12, qBph4.1, Bph3, Bph35, qBph4.2, Bph15, Bph36, qBph4, Bph20(t), and Bph17) were clustered between 4.44 and 9.38 Mb on chromosome 4S [2,3,33,[38][39][40][41][42][43][44]; and Bph27(t), Bph6, Bph44, Bph34, and Bph42 were clustered on chromosome 4L between 20.60 and 21.80 Mb [24,37,[45][46][47]. The Bph37 that from SE382, Bph25, bph29, Bph32 and bph4 were present on chromosome 6S between 0.21 and 1.47 Mb [22,[48][49][50][51].…”

“…4.44 and 9.38 Mb on chromosome 4S [2,3,33,[38][39][40][41][42][43][44]; and Bph27(t), Bph6, Bph44, Bph34, and Bph42 were clustered on chromosome 4L between 20.60 and 21.80 Mb [24,37,[45][46][47]. The Bph37 that from SE382, Bph25, bph29, Bph32 and bph4 were present on chromosome 6S between 0.21 and 1.47 Mb [22,[48][49][50][51].…”

Latest Review Papers in Molecular Plant Sciences 2023

“…Genetic analysis led to the identification of 70 genes and a quantitative trait locus (QTL) associated with BPH resistance in rice. However, efficient utilization of these markers required gene/QTL duplication in as many as 26 known cases [31][32][33][34]. The insights from this review could advance the development of sustainable biological control strategies for managing BPH infestations.…”