Jingguo Wang

Dynamic QTL analysis of the Na+ content, K+ content, and Na+/K+ ratio in rice roots during the field growth under salt stress

Rice (Oryza sativa L.) is seriously impacted by global soil salinization. To determine the quantitative trait loci (QTLs) related to salt tolerance in rice roots, F2:3 and BC1F2:3 populations derived from a cross between the cv. Dongnong 425 of high quality and yield and the salt-tolerant cv. Changbai 10, were studied at different development stages. Two genetic linkage maps of F2:3 and BC1F2:3 populations were constructed. A 66 mM NaCl solution was used to irrigate the field and to analyze the dynamic QTL of some rice root traits. Using unconditional and conditional QTL mapping methods, 30 unconditional QTLs and 16 conditional QTLs related to the 6 root traits were detected on the 9 rice chromosomes during different developmental stages. Fourteen pairs of unconditional and conditional QTLs were detected at the identical developmental stage in the identical population. A number of QTLs were detected at different developmental stages, however, many did not appear at the last stage. Remarkably, qRKC1 appeared continuously at multiple stages in both the populations suggesting its key role in regulating the salt tolerance of rice roots.

Genetic diversity and genetic relationships of japonica rice varieties in Northeast Asia based on SSR markers

Genetic diversity and the relationship among nine japonica rice groups consisting of 288 landraces and varieties in different geographical origins of Northeast Asia (China, Japan, Korea, Democratic Peoples Republic of Korea) and the Russian Far East district of the Russian Federation were evaluated with 154 simple sequence repeat (SSR) markers. A total of 823 alleles were detected. The observed allele numbers (Na) per locus, Neis gene diversity (He) and the polymorphism information content (PIC) ranged from 2 to 9, 0.061 to 0.869 and 0.060 to 0.856, with an average of 5.344, 0.624 and 0.586, respectively. Five SSR loci, RM1350, RM1369, RM257, RM336 and RM1374, provided the highest PIC values and are potential for exploring the genetic diversity of rice cultivars in Northeast Asia. Molecular variance analysis showed that a significant difference existed both among groups (91.6%) and within each group (8.4%). The low genetic variation within each group indicated that the gene pool is narrow and alien genetic variation should be introduced into the rice breeding program in Northeast Asia. Based on the He and PIC values, the nine groups were ranked in a descending order: Heilongjiang landraces, Jilin landraces, Japanese improved varieties, Heilongjiang improved varieties, Russian Far East district of the Russian Federation improved varieties, Liaoning improved varieties, Jilin improved varieties, Korean improved varieties and Democratic Peoples Republic of Korea improved varieties. The nine groups were further divided into three subgroups and the 288 varieties into five clusters. This study provided information for parent selection in order to broaden the gene pool of the japonica rice germplasm in Northeast Asia.

Genetic dissection of the developmental behavior of plant height in rice under different water supply conditions

Abstract Plant height (PH) is one of the most important agronomic traits of rice, as it directly affects the lodging resistance and the high yield potential. Meanwhile, PH is often constrained by water supply over the entire growth period. In this study, a recombinant inbred line (RIL) derived from Xiaobaijingzi and Kongyu 131 strains grown under drought stress and with normal irrigation over 2 yr (2013 and 2014), respectively (regarded as four environments), was used to dissect the genetic basis of PH by developmental dynamics QTL analysis combined with QTL×environment interactions. QTLs with net effects excluding the accumulated effects were detected to explore the relationship between gene×gene interactions and gene×environment interactions in specific growth period. A total of 26 additive QTLs (A-QTLs) and 37 epistatic QTLs (E-QTLs) associated with PH were detected by unconditional and conditional mapping over seven growth periods. qPH-2-3, qPH-4-3, qPH-6-1, qPH-7-1, and qPH-12-5 could be detected by both unconditional and conditional analyses. qPH-4-3 and qPH-7-5 were detected in four stages (periods) to be sequentially expressed QTLs controlling PH continuous variation. QTLs with additive effects (A-QTLs) were mostly expressed in the period S3|S2 (the time interval from stages 2 to 3), and QTL×environment interactions performed actively in the first three stages (periods) which could be an important developmental period for rice to undergo external morphogenesis during drought stress. Several QTLs showed high adaptability for drought stress and many QTLs were closely related to the environments such as qPH-3-5, qPH-2-2 and qPH-6-1. 72.5% of the QTLs with a and aa effects detected by conditional analysis were under drought stress, and the PVE of QTLs detected by conditional analysis under drought stress were also much higher than that under normal irrigation. We infer that environments would influence the detection results and sequential expression of genes was highly influenced by environments as well. Many QTLs (qPH-1-2, qPH-3-5, qPH-4-1, qPH-2-3) coincident with previously identified drought resistance genes. The result of this study is helpful to elucidating the genetic mechanism and regulatory network underlying the development of PH in rice and providing references to marker assisted selection.

Transcriptome analysis of two contrasting rice cultivars during alkaline stress.

Soil alkalinity greatly affects plant growth and crop productivity. Although RNA-Seq analyses have been conducted to investigate genome-wide gene expression in response to alkaline stress in many plants, the expressions of alkali-responsive genes in rice have not been previously investigated. In this study, the transcriptomic data between an alkaline-tolerant (WD20342) and an alkaline-sensitive (Caidao) rice cultivar were compared under alkaline stress conditions. A total of 962 important alkali-responsive (IAR) genes from highly differentially expressed genes (DEGs) were identified, including 28 alkaline-resistant cultivar-related genes, 771 alkaline-sensitive cultivar-related genes and 163 cultivar-non-specific genes. Gene ontology (GO) analysis indicated the enrichment of IAR genes involved in various stimulus or stress responses. According to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, the IAR genes were related primarily to plant hormone signal transduction and biosynthesis of secondary metabolites. Additionally, among these 962 IAR genes, 74 were transcription factors and 15 occurred with differential alternative splicing between the different samples after alkaline treatment. Our results provide a valuable resource on alkali-responsive genes and should benefit the improvement of alkaline stress tolerance in rice.