Nitrogen is an essential nutrient for crop growth and development. Although the functions of several genes associated with nitrogen deficiency tolerance have been studied, many genetic components remain unknown. In this study, 190 North Korean (NK) rice genotypes were used to identify genes linked to nitrogen deficiency resistance. The NK population was hydroponically cultivated for 31 days under normal nitrogen (NN) and low nitrogen (LN) conditions. After this period, phenotypic evaluations were conducted on six agronomic traits (SPAD, shoot length, root length, shoot fresh weight, root fresh weight, and tiller number). A genome-wide association study (GWAS) was performed using the phenotypic values and resequencing data from 190 NK rice genotypes. As a result, 107 significant lead SNPs were identified. Among the genes related to these lead SNPs, 12 previously identified NUE-related genes for nitrogen use efficiency (NUE) and 6 unknown candidate genes exhibited significant differences in haplotype analysis. Nine of the 12 known genes (
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Rice yield is severely affected by phosphorus (P) deficiency, and plants have evolved various strategies to cope with this limitation. While some rice genotypes are adapted to low phosphate (Pi) availability, others remain sensitive to Pi deficiency. In this study, we conducted a genome-wide association study (GWAS) using a hydroponically cultivated population of 190 North Korean (NK) rice plants to identify genes associated with phosphorus use efficiency (PUE) and Pi deficiency tolerance. The rice plants were grown in Yoshida nutrient media with either full (10 mg/L) or low-P (1 mg/L) concentrations for 40 days. The phenotypic response to Pi deficiency was assessed at the seedling stage, followed by an evaluation of eight agricultural traits: chlorophyll content (SPAD), shoot length (SL), shoot fresh weight (SFW), shoot dry weight (SDW), root fresh weight (RFW), root dry weight (RDW), and tiller number (TN). The GWAS analysis revealed a total of 166 significant lead SNPs, with six located near known genes for Pi deficiency tolerance:
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SNP-based markers have been widely used to identify tolerant varieties harboring major genes related to abiotic stress tolerance. Here, we developed Fluidigm markers for the core set of SNPs underlying tolerance to abiotic stresses such as salinity, drought, anaerobic germination and submergence. The core set of SNPs was selected from the major genes and/or QTLs for the abiotic stresses previously reported in rice;
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Seedling vigor in drought stress conditions is an important characteristic of the dry direct-seeded rice system. The drought stress in the seedling stage disrupts seed germination and delays the establishment of seedlings. However, little is known about the genetic mechanism of seedling vigor in drought conditions. The identification of quantitative trait loci (QTL) was conducted using 162 recombinant inbred lines (RILs) derived from a cross between two rice varieties—a Tongil-type Milyang23 and a temperate japonica Tong88-7. The seedling vigor of these RILs was characterized by measuring 10 morphological traits of the seedlings grown under drought conditions. The Tong88-7 seedlings showed significantly higher values than the Milyang23 seedlings for all traits. The genotyping-by-sequencing method was used to construct a map of 6140 single nucleotide polymorphisms. Six main-effect QTLs (M-QTLs) associated with seedling vigor traits under drought stress were identified on chromosomes 9 and 11. In particular, five out of these six QTLs were located on chromosome 11, explaining the phenotypic variances of 4.3% through 10.1%. In addition, 21 epistatic QTLs (E-QTLs) were detected, and the 27 loci involved in this interaction were distributed on 11 chromosomes. Both M-QTLs and E-QTLs detected in this study would be useful in breeding programs to develop elite rice varieties especially adapted to dry direct-seeded rice system.
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