Background Rice is considered as a salt-sensitive plant, particularly at early vegetative stage, and its production is suffered from salinity due to expansion of salt affected land in areas under cultivation. Hence, significant increase of rice productivity on salinized lands is really necessary. Today genome-wide association study (GWAS) is a method of choice for fine mapping of QTLs involved in plant responses to abiotic stresses including salinity stress at early vegetative stage. In this study using > 33,000 SNP markers we identified rice genomic regions associated to early stage salinity tolerance. Eight salinity-related traits including shoot length (SL), root length (RL), root dry weight (RDW), root fresh weight (RFW), shoot fresh weight (SFW), shoot dry weight (SDW), relative water content (RWC) and TW, and 4 derived traits including SL-R, RL-R, RDW-R and RFW-R in a diverse panel of rice were evaluated under salinity (100 mM NaCl) and normal conditions in growth chamber. Genome-wide association study (GWAS) was applied based on MLM(+Q + K) model. Results Under stress conditions 151 trait-marker associations were identified that were scattered on 10 chromosomes of rice that arranged in 29 genomic regions. A genomic region on chromosome 1 (11.26 Mbp) was identified which co-located with a known QTL region SalTol1 for salinity tolerance at vegetative stage. A candidate gene (Os01g0304100) was identified in this region which encodes a cation chloride cotransporter. Furthermore, on this chromosome two other candidate genes, Os01g0624700 (24.95 Mbp) and Os01g0812000 (34.51 Mbp), were identified that encode a WRKY transcription factor (WRKY 12) and a transcriptional activator of gibberellin-dependent alpha-amylase expression (GAMyb), respectively. Also, a narrow interval on the same chromosome (40.79–42.98 Mbp) carries 12 candidate genes, some of them were not so far reported for salinity tolerance at seedling stage. Two of more interesting genes are Os01g0966000 and Os01g0963000, encoding a plasma membrane (PM) H+-ATPase and a peroxidase BP1 protein. A candidate gene was identified on chromosome 2 (Os02g0730300 at 30.4 Mbp) encoding a high affinity K+ transporter (HAK). On chromosome 6 a DnaJ-encoding gene and pseudouridine synthase gene were identified. Two novel genes on chromosome 8 including the ABI/VP1 transcription factor and retinoblastoma-related protein (RBR), and 3 novel genes on chromosome 11 including a Lox, F-box and Na+/H+ antiporter, were also identified. Conclusion Known or novel candidate genes in this research were identified that can be used for improvement of salinity tolerance in molecular breeding programmes of rice. Further study and identification of effective genes on salinity tolerance by the use of candidate gene-association analysis can help to precisely uncover the mechanisms of salinity tolerance at molecular level. A time dependent relationship between salt tolerance and expression level of candidate genes could be recognized.

Water and soil salinity as the main abiotic stresses decrease crop yield and restrict the use of agricultural lands. In order to assess salt stress effect on seedling growth of rice and to select more tolerant rice genotypes, a factorial experiment was performed at two levels of NaCl namely non-stress (EC 1.2 dS m −1 ) and salt-stress (EC 10 dS m −1 ) in hydroponics with an international rice collection consisted of 155 varieties. Seven stress tolerance indices including STI, SSI, HM, RDI, SSPI, ATI and TOL were used to identify salt tolerant genotypes. The results of variance analysis showed that the effect of genotypes (G), Salt treatment (T) and G×T interaction were significant for all investigated traits (except for the effect of genotypes on shoot length). Under salt stress most genotypes showed similar trend of salt response, i.e. reduction in all traits. The results also revealed that dry weight (DW) was less affected than fresh weight (FW), and the shoot weight (SW) was affected more than the root weight (RW), indicating that shoot growth is more sensitive than root growth to salt stress. The Na + , K + and Na + :K + ratio were increased more than 713%, reduced 22% and increased more than 996% under salt stress, respectively. Four stress tolerance indices including MP, HM, GMP and STI showed highest correlation with each other and also with plant performance (Z-scores) under both normal and stress conditions; thus each of these indices can be used as the suitable indicators for screening salt tolerant genotypes. Based on the results, genotypes #84, #30 and #48 showed the highest performance and STI under salinity condition, so they have considerable potential to improve salt tolerance in rice breeding programs. In addition, genotypes #178, #198 and #6 with the lowest values of STI were found to be intolerant genotypes to salt stress.

Cytoplasmic male sterility (CMS) is a cornerstone of hybrid production in many crops. In three-line hybrid systems, use of CMS, maintainer, and fertility restorer lines is necessary for production of hybrid seeds. Limited resources of CMS and low variation of CMS lines cause genetic vulnerability to pathogens. Therefore, diversifying the CMS sources is indispensible for a sustainable production system of hybrid seed. In this study, we attempted for the first time to transfer CMS into maintainer line Yosen B in restricted generations using the marker-assisted backcrossing (MABC) method. The resultant F 1 hybrid of IR68897 A/Yosen B cross was backcrossed to Yosen B, and CMS plants in each backcross generation (from BC 1 F 1 to BC 3 F 1 ) were selected based on phenotyping test and MABC. Molecular assessment of backcross progenies was conducted using a mitochondrial CMS-specific marker and 34 polymorphic nuclear simple-sequence repeat (SSR) markers in early generations (from BC 1 F 1 to BC 2 F 1 ) and was continued using 9 additional SSRs and 82 inter-simple sequence repeat (ISSR) markers in BC 3 F 1 . A MABC strategy could successfully recover the recurrent parent genome (RPG) in BC 3 F 1 generation, and decreased heterozygosity of final CMS plants. Restorability test with known wild-abortive restorer lines (viz. IR36 and IR24) showed that combination of Yosen A  IR24 could produce highly fertile F 1 hybrid. Evaluation of some important agronomic traits of the final CMS line (BC 4 F 1 ) at field condition showed that it was comparable to the original maintainer fertile counterpart. Phenotypic and marker-assisted selections could considerably decrease the time needed for full recovery of RPG so that final CMS line could show a high similarity to original fertile counterpart.

Background Rice is considered as a salt-sensitive plant, particularly at early vegetative stage, and its production is suffered from salinity due to expansion of salt affected land in areas under cultivation. Hence, significant increase of rice productivity on salinized lands is really necessary. Today genome-wide association study (GWAS) is a method of choice for fine mapping of QTLs involved in plant responses to abiotic stresses including salinity stress at early vegetative stage. In this study using > 33,000 SNP markers we identified rice genomic regions associated to early stage salinity tolerance. Eight salinity-related traits including SL, RL, RDW, RFW, SFW, SDW, RWC and TW in a diverse panel of rice consisted of 202 varieties were evaluated under salinity (100 mM NaCl) and normal conditions in growth chamber. Genome-wide association study (GWAS) was applied based on MLM(+ Q + K) model.Results Under stress conditions 151 trait-marker associations were identified that were scattered on 10 chromosomes of rice that arranged in 29 genomic regions. A genomic region on chromosome 1 (11.26 Mbp) was identified which co-located with a known QTL region SalTol1 for salinity tolerance at vegetative stage. A candidate gene (Os01g0304100) was identified in this region which encodes a cation chloride cotransporter. Furthermore, on this chromosome two other candidate genes, Os01g0624700 (24.95 Mbp) and Os01g0812000 (34.51 Mbp), were identified that encode a WRKY transcription factor (WRKY 12) and a transcriptional activator of gibberellin-dependent alpha-amylase expression (GAMyb), respectively. Also, a narrow interval on the same chromosome (40.79–42.98 Mbp) carries 12 candidate genes, some of them were not so far reported for salinity tolerance at seedling stage. Two of more interesting genes are Os01g0966000 and Os01g0963000, encoding a plasma membrane (PM) H+-ATPase and a peroxidase BP1 protein. On chromosome 6 a DnaJ-encoding gene and pseudouridine synthase gene were identified. Two novel genes on chromosome 8 including the ABI/VP1 transcription factor and retinoblastoma-related protein (RBR), and 3 novel genes on chromosome 11 including a Lox, F-box and Na+/H+ antiporter, were also identified.Conclusion The results for RDW and RFW were found more important than other traits, and known or novel candidate genes in this research can be used for improvement of salinity tolerance in molecular breeding programmes. Further study and identification of effective genes on salinity tolerance by the use of candidate gene-association analysis can help to precisely uncover the mechanisms of salinity tolerance at molecular level.

Background: Rice is considered as a salt-sensitive plant, particularly at early vegetative stage, and its production is suffered from salinity due to expansion of salt affected land in areas under cultivation. Hence, significant increase of rice productivity on salinized lands is really necessary. Today genome-wide association study (GWAS) is a method of choice for fine mapping of QTLs involved in plant responses to abiotic stresses including salinity stress at early vegetative stage. In this study using >33,000 SNP markers we identified rice genomic regions associated to early stage salinity tolerance. Eight salinity-related traits including shoot length (SL), root length (RL), root dry weight (RDW), root fresh weight (RFW), shoot fresh weight (SFW), shoot dry weight (SDW), relative water content (RWC) and TW, and 4 derived traits including SL-R, RL-R, RDW-R and RFW-R in a diverse panel of rice consisted of 202 varieties were evaluated under salinity (100 mM NaCl) and normal conditions in growth chamber. Genome-wide association study (GWAS) was applied based on MLM(+Q+K) model.Results: Under stress conditions 151 trait-marker associations were identified that were scattered on 10 chromosomes of rice that arranged in 29 genomic regions. A genomic region on chromosome 1 (11.26 Mbp) was identified which co-located with a known QTL region SalTol1 for salinity tolerance at vegetative stage. A candidate gene ( Os01g0304100 ) was identified in this region which encodes a cation chloride cotransporter. Furthermore, on this chromosome two other candidate genes, Os01g0624700 (24.95 Mbp) and Os01g0812000 (34.51 Mbp), were identified that encode a WRKY transcription factor ( WRKY 12 ) and a transcriptional activator of gibberellin-dependent alpha-amylase expression ( GAMyb ), respectively. Also, a narrow interval on the same chromosome (40.79-42.98 Mbp) carries 12 candidate genes, some of them were not so far reported for salinity tolerance at seedling stage. Two of more interesting genes are Os01g0966000 and Os01g0963000 , encoding a plasma membrane (PM) H + -ATPase and a peroxidase BP1 protein. A candidate gene was identified on chromosome 2 ( Os02g0730300 at 30.4 Mbp) encoding a high affinity K + transporter (HAK). On chromosome 6 a DnaJ-encoding gene and pseudouridine synthase gene were identified. Two novel genes on chromosome 8 including the ABI/VP1 transcription factor and retinoblastoma-related protein (RBR), and 3 novel genes on chromosome 11 including a Lox, F-box and Na + /H + antiporter, were also identified.Conclusion: Known or novel candidate genes in this research were identified that can be used for improvement of salinity tolerance in molecular breeding programmes of rice. Further study and identification of effective genes on salinity tolerance by the use of candidate gene-association analysis can help to precisely uncover the mechanisms of salinity tolerance at molecular level. A time dependent relationship between salt tolerance and expression level of candidate genes could be recognized.