A first set of 25 NILs carrying ten BPH resistance genes and their pyramids was developed in the background of indica variety IR24 for insect resistance breeding in rice. Brown planthopper (Nilaparvata lugens Stal.) is one of the most destructive insect pests in rice. Development of near-isogenic lines (NILs) is an important strategy for genetic analysis of brown planthopper (BPH) resistance (R) genes and their deployment against diverse BPH populations. A set of 25 NILs with 9 single R genes and 16 multiple R gene combinations consisting of 11 two-gene pyramids and 5 three-gene pyramids in the genetic background of the susceptible indica rice cultivar IR24 was developed through marker-assisted selection. The linked DNA markers for each of the R genes were used for foreground selection and confirming the introgressed regions of the BPH R genes. Modified seed box screening and feeding rate of BPH were used to evaluate the spectrum of resistance. BPH reaction of each of the NILs carrying different single genes was variable at the antibiosis level with the four BPH populations of the Philippines. The NILs with two- to three-pyramided genes showed a stronger level of antibiosis (49.3-99.0%) against BPH populations compared with NILs with a single R gene NILs (42.0-83.5%) and IR24 (10.0%). Background genotyping by high-density SNPs markers revealed that most of the chromosome regions of the NILs (BCF) had IR24 genome recovery of 82.0-94.2%. Six major agronomic data of the NILs showed a phenotypically comparable agronomic performance with IR24. These newly developed NILs will be useful as new genetic resources for BPH resistance breeding and are valuable sources of genes in monitoring against the emerging BPH biotypes in different rice-growing countries.

Adaptation of temperate japonica rice varieties to tropical regions is impeded by extremely early flowering probably due to photoperiod change from long to short. However, constant breeding efforts led to development of temperate japonica varieties adapted to tropical/subtropical regions, but the genetic factor underlying this is still elusive. We analyzed the 45 diverse rice accessions and 12 tropical-adapted temperate japonica lines for the allele types of seven major flowering genes Hd1, OsPPR37, DTH8, Ghd7, Ehd1, RFT1, and Hd3a and flowering time under three different field conditions in temperate and tropical locations. The accessions originated from the tropical/subtropical regions preferred the non-functional alleles of Hd1 and not other flowering genes. The genetic effect analysis of each gene showed that only the functional Hd1 caused early flowering in the tropical location. All 12 temperate japonica breeding lines adapted to the tropics possessed the loss-of-function alleles of Hd1 with no change of other flowering genes compared to common Korean temperate japonica varieties. A phylogenetic analysis using 2,918 SNP data points revealed that the genome status of the 12 breeding lines were very similar to Korean temperate japonica varieties. These results indicate that the functional Hd1 alleles of temperate japonica varieties induced extremely early flowering in the tropics and the non-functional hd1 alleles brought about the adaptation of temperate japonica rice to tropical regions.

BackgroundRice (Oryza sativa L.) is the staple food for more than 3.5 billion people, mainly in Asia. Brown planthopper (BPH) is one of the most destructive insect pests of rice that limits rice production. Host-plant resistance is one of the most efficient ways to overcome BPH damage to the rice crop.ResultsBPH bioassay studies from 2009 to 2015 conducted in India and at the International Rice Research Institute (IRRI), Philippines, revealed that the cultivar CR2711–76 developed at the National Rice Research Institute (NRRI), Cuttack, India, showed stable and broad-spectrum resistance to several BPH populations of the Philippines and BPH biotype 4 of India. Genetic analysis and fine mapping confirmed the presence of a single dominant gene, BPH31, in CR2711–76 conferring BPH resistance. The BPH31 gene was located on the long arm of chromosome 3 within an interval of 475 kb between the markers PA26 and RM2334. Bioassay analysis of the BPH31 gene in CR2711–76 was carried out against BPH populations of the Philippines. The results from bioassay revealed that CR2711–76 possesses three different mechanisms of resistance: antibiosis, antixenosis, and tolerance. The effectiveness of flanking markers was tested in a segregating population and the InDel type markers PA26 and RM2334 showed high co-segregation with the resistance phenotype. Foreground and background analysis by tightly linked markers as well as using the Infinium 6 K SNP chip respectively were applied for transferring the BPH31 gene into an indica variety, Jaya. The improved BPH31-derived Jaya lines showed strong resistance to BPH biotypes of India and the Philippines.ConclusionThe new BPH31 gene can be used in BPH resistance breeding programs on the Indian subcontinent. The tightly linked DNA markers identified in the study have proved their effectiveness and can be utilized in BPH resistance breeding in rice.Electronic supplementary materialThe online version of this article (doi:10.1186/s12284-017-0178-x) contains supplementary material, which is available to authorized users.

Rice is the most important staple food crop, and it feeds more than half of the world population. Brown planthopper (BPH) is a major insect pest of rice that causes 20–80% yield loss through direct and indirect damage. The identification and use of BPH resistance genes can efficiently manage BPH. A molecular marker-based genetic analysis of BPH resistance was carried out using 101 BC1F5 mapping population derived from a cross between a BPH-resistant indica variety Khazar and an elite BPH-susceptible line Huang–Huan–Zhan. The genetic analysis indicated the existence of Mendelian segregation for BPH resistance. A total of 702 high-quality polymorphic single nucleotide polymorphism (SNP) markers, genotypic data, and precisely estimated BPH scores were used for molecular mapping, which resulted in the identification of the BPH38(t) locus on the long arm of chromosome 1 between SNP markers 693,369 and id 10,112,165 of 496.2 kb in size with LOD of 20.53 and phenotypic variation explained of 35.91%. A total of 71 candidate genes were predicted in the detected locus. Among these candidate genes, LOC_Os01g37260 was found to belong to the FBXL class of F-box protein possessing the LRR domain, which is reported to be involved in biotic stress resistance. Furthermore, background analysis and phenotypic selection resulted in the identification of introgression lines (ILs) possessing at least 90% recurrent parent genome recovery and showing superior performance for several agro-morphological traits. The BPH resistance locus and ILs identified in the present study will be useful in marker-assisted BPH resistance breeding programs.Electronic supplementary materialThe online version of this article (10.1007/s10681-019-2506-2) contains supplementary material, which is available to authorized users.

Blast and bacterial leaf blight are major diseases of rice that limit grain yield significantly. These two devastating biotic stresses have to be controlled to meet the demand for 23 % more rice production by 2035 to feed the increasing number of rice consumers. Incorporating appropriate disease resistance genes into elite varieties is considered as the best method to enhance crop resistance. Molecular markers play an important role in multiple gene pyramiding programs to select desirable genotypes with targeted genes. Two major resistance genes, Pita and xa5, for blast and bacterial leaf blight races, respectively, have been used in many gene pyramiding programs. However, simple PCR-based functional codominant markers have not been reported for these genes. Hence, in the present study, time-and costeffective codominant markers for Pita and xa5 have been developed and validated in segregating populations. High-throughput screening has been demonstrated using parallel capillary electrophoresis to replace laborious gel-based electrophoresis. Additionally, the presence of Pita and xa5 alleles was evaluated with 260 diverse rice varieties that were collected from different parts of the world. Of the 260 cultivars tested, 55 were identified with the Pita resistance allele while all the tested cultivars had the susceptible Xa5 allele. The identified Pita allele-derived cultivars can be used as an alternative resistance source for blast disease. The newly developed Pita and xa5 functional markers will help toward tracking the two target genes for blast and bacterial leaf blight resistance in breeding programs.