Salinity has a significant impact on rice production in coastal, arid and semi-arid areas in many countries, including countries growing temperate rice, such as Kazakhstan. Recently, the complete genomes of 3000 rice accessions were sequenced through the 3 K rice genome project, and this set included 203 temperate japonica rice accessions. To identify salinity-tolerant germplasm and related genes for developing new salinity-tolerant breeding lines for the temperate japonica rice growing regions, we evaluated the seedling stage salinity tolerance of these sequenced temperate japonica rice accessions, and conducted genome-wide association studies (GWAS) for a series of salinity tolerance related traits. There were 27 accessions performed well (SES < 5.0) under moderate salinity stress (EC12), and 5 accessions were tolerant under both EC12 and EC18. A total of 26 QTLs were identified for 9 measured traits. Eleven of these QTLs were co-located with known salinity tolerance genes. QTL/gene clusters were observed on chromosome 1, 2, 3, 6, 8 and 9. Six candidate genes were identified for five promising QTLs. The alleles of major QTL Saltol and gene O S HKT1;5 (SKC1) for Na+/K+ ratio identified in indica rice accessions were different from those in the temperate japonica rice accessions used in this study. Salinity tolerant temperate japonica rice accessions were identified in this study, these accessions are important resources for breeding programs. SNPs located in the promising QTLs and candidate genes could be used for future gene validation and marker assisted selection. This study provided useful information for future studies on genetics and breeding of salinity tolerance in temperate japonica rice.

Rice blast caused by pathogenic fungus Magnaporthe oryzae is one of the most serious diseases in rice. The pyramiding of effective resistance genes into rice varieties is a potential approach to reduce the damage of blast disease. In this study, combinations of three resistance genes, Pigm, Pi48 and Pi49, were introduced into a thermo-sensitive genic male sterile (PTGMS) line Chuang5S through marker-assisted selection. The results showed that the blast resistance of improved lines increased significantly compared with Chuang5S, and the three gene pyramiding lines (Pigm + Pi48 + Pi49) had higher rice blast resistance level than monogenic line and digenic lines (Pigm +Pi48, Pigm + Pi49). The genetic backgrounds of the improved lines were highly similar (>90%) to the recurrent parent Chuang5S by using the RICE10K SNP chip. In addition, agronomic traits evaluation also showed pyramiding lines with two or three genes similar to Chuang5S. The yields of the hybrids developed from improved PTGMS lines and Chuang5S are not significantly different. The newly developed PTGMS lines can be practically used for the breeding of parental lines and hybrid varieties with broad spectrum blast resistance.

Extreme weather events, especially heat waves, have become more frequent with global warming. High temperature significantly affects world food security by decreasing crop yield. Rice is intensively planted in tropical and subtropical areas in Asia, where high temperature has become a major factor affecting rice production. Rice is sensitive to high temperature, especially at booting and flowering stages. Rice varieties tolerant of high temperature are rare, and only a few heat-tolerant rice varieties have been identified. High temperature at booting and flowering stages causes sterile pollen, decreased pollen shedding, and poor pollen germination, which finally lead to a yield decrease. Heat-tolerant QTLs have been identified in different studies, but new breeding lines with considerable heat tolerance have not been bred using identified heat-tolerance donors and QTLs. Research on heat-tolerant donor identification, QTL mapping, gene cloning, and large-scale phenotyping technology is important for developing heat-tolerant rice varieties.

Temperate japonica rice plays a very important role in food security. In this study, a set of 191 temperate japonica accessions from 30 countries were planted in two sites in China, and 12 agronomic traits were measured. The results showed a wide range of variation for the traits measured. Most of the accessions are short; three accessions with large panicles and seven accessions with large grains were identified. Sixty-two quantitative trait loci (QTLs) were identified for 12 traits that were measured. Among them, twenty-one QTLs were identified in both experiments, and 41 QTLs were identified in only one site. Some known genes are located in the QTL regions identified in our study. SNP markers for grain size were identified and could be efficiently used for breeding selection. This study provided useful information for future gene validation and marker assisted selection for some important agronomic traits of temperate japonica rice.