BackgroundSalinity 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.ResultsThere 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 OSHKT1;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.ConclusionSalinity 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.Electronic supplementary materialThe online version of this article (10.1186/s12863-017-0590-7) contains supplementary material, which is available to authorized users.

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A b s t r a c tAbout 25 % of the entire land surface is represented by saline soils, and up to 90 % of the total irrigated area -in some regions of Central Asia and the Caucasus, Ukraine and Kazakhstan. Rice-growing region of the Republic of Kazakhstan is also located in the area with high salinity. A challenge for rice growing in Kazakhstan is deteriorating humus and reclamation of soil, rise in soil secondary salinity and degradation. In Kyzylorda region, pollution of surface (up to 3-5 g/l) and ground water (up to 6-7 g/l) by salt residues reaches a critical point. The dominating sulfatechloride-sodium type of salinity is especially toxic for crops. Akdalinski and Karatal zones of irrigation in the Almaty region are also located within the provinces of sulfate-soda and boric biogeochemical soil salinity. According the data of Kazakh Rice Research Institute, in recent years the rice yields and yield quality have sharply decreased -from 50 to 35-48 centners per hectare, and from 65 to 45-50 % of the groats output, respectively. In this regard, the rice breeding for salt tolerance is the most important to ensure food security in Kazakhstan. The objective of our study was the evaluation and selection a promising starting material of rice resistant to different types of salinity. To this end, we studied the rice (Oryza sativa L.) varieties, collection samples and their hybrid combinations of different generations derived from Russia, Kazakhstan and Philippine (34 genotypes in total). For the initial assessment at the seedling stage we used the laboratory screening for tolerance to various types of salinity, i.e. chloride, sulphate and carbonate. Saline stress negatively affected seedling growth and total weight in the studied samples. It was revealed that the carbonate type of salinity is the most toxic for rice plants; the chloride and sulfate types were less adverse. The hybrid collection sample F 2 Khankai 429 ½ 4-09 and as well as varieties Marzhan and Madina accumulated the highest percentage of biomass compared to the control at the salinity of all three types. Therefore, these genotypes are valuable in selection for salt tolerance. Molecular screening of chromosomal DNA regions linked to quantitative trait loci of salt tolerance (Saltol QTL) by PCR with microsatellite markers closely linked to the target chromosomal regions, RM 493 and AP 3206, showed RM 493 to produce polymorphism which allowed to distinguish the studied genotypes contrasting in salt tolerance. Thus RM 493 is informative to rank the rice genetic plasma by salt tolerance.Keywords: Oryza sativa L., rice, chloride salinity, sulfate salinization, carbonate salinity, molecular screening for salt tolerance, SSR markers, selection About 950 million hectares of agricultural lands in the world are saline,

The genus Allium L comprises over 1000 species with important nutritional, medicinal and horticultural applications. The natural flora of Kazakhstan is rich in Allium species, including the wild long-pointed onion, A. longicuspis and cultivated A. sativum garlic varieties. It has been hypothesized that A. longicupis is ancestral to A. sativum. We investigated genetic polymorphism in samples of A. longicupis and the A. sativum cultivars "Niki" and "Merey" using start codon targeted polymorphism analysis. Nuclear ribosomal DNA fragments were purified, amplified and tested with 25 primers, finally selecting 12 primers that identified polymorphisms. DNA samples were sequenced, electrophoresed and cluster analysis performed by the construction of dendrograms and principal component analysis. The karyotypes of the different samples were also compared. The results showed that the samples of A. longicupis from natural populations did not differ significantly from those of the cultivated garlic varieties. The results indicate that A. longicupis can be considered a feral, rather than an ancestral, form of A. sativum. These findings have implications both for the breeding and cultivation of garlic varieties and for the taxonomy of the Allium genus.

Although there is low precipitation in Kazakhstan, rice is grown in regions serviced by irrigation canals. And breeding has begun in order to reduce the cost of importing glutinous rice. To develop glutinous rice cultivars efficiently, we need information on the haplotypes of Wx and Alk genes that affect eating quality. We investigated the haplotypes and amylopectin chain-length distribution in the first glutinous rice breeding lines developed in Kazakhstan. Such information could be useful to other countries starting glutinous rice breeding using parents possessing variation in Wx and Alk haplotypes.