Guifu Liu

QTL × environment interactions in rice. I. Heading date and plant height

One hundred twenty six doubled-haploid (DH) rice lines were evaluated in nine diverse Asian environments to reveal the genetic basis of genotype × environment interactions (GEI) for plant height (PH) and heading date (HD). A subset of lines was also evaluated in four water-limited environments, where the environmental basis of G × E could be more precisely defined. Responses to the environments were resolved into individual QTL × environment interactions using replicated phenotyping and the mixed linear-model approach. A total of 37 main-effect QTLs and 29 epistatic QTLs were identified. On average, these QTLs were detectable in 56% of the environments. When detected in multiple environments, the main effects of most QTLs were consistent in direction but varied considerably in magnitude across environments. Some QTLs had opposite effects in different environments, particularly in water-limited environments, indicating that they responded to the environments differently. Inconsistent QTL detection across environments was due primarily to non- or weak-expression of the QTL, and in part to significant QTL × environment interaction effects in the opposite direction to QTL main effects, and to pronounced epistasis. QTL × environment interactions were trait- and gene-specific. The greater GEI for HD than for PH in rice were reflected by more environment-specific QTLs, greater frequency and magnitude of QTL × environment interaction effects, and more pronounced epistasis for HD than for PH. Our results demonstrated that QTL × environment interaction is an important property of many QTLs, even for highly heritable traits such as height and maturity. Information about QTL × environment interaction is essential if marker-assisted selection is to be applied to the manipulation of quantitative traits.

Identification of QTL for growth- and grain yield-related traits in rice across nine locations of Asia

Abstract. Rice double-haploid (DH) lines of an indica and japonica cross were grown at nine different locations across four countries in Asia. Genotype-by-environment (G × E) interaction analysis for 11 growth- and grain yield-related traits in nine locations was estimated by AMMI analysis. Maximum G × E interaction was exhibited for fertility percentage number of spikelets and grain yield. Plant height was least affected by environment, and the AMMI model explained a total of 76.2% of the interaction effect. Mean environment was computed by averaging the nine environments and subsequently analyzed with other environments to map quantitative trait loci (QTL). QTL controlling the 11 traits were detected by interval analysis using mapmaker/qtl. A threshold LOD of ≥3.20 was used to identify significant QTL. A total of 126 QTL were identified for the 11 traits across nine locations. Thirty-four QTL common in more than one environment were identified on ten chromosomes. A maximum of 44 QTL were detected for panicle length, and the maximum number of common QTL were detected for days to heading detected. A single locus for plant height (RZ730-RG810) had QTL common in all ten environments, confirming AMMI results that QTL for plant height were affected the least by environment, indicating the stability of the trait. Two QTL were detected for grain yield and 19 for thousand-grain weight in all DH lines. The number of QTL per trait per location ranged from zero to four. Clustering of the QTL for different traits at the same marker intervals was observed for plant height, panicle number, panicle length and spikelet number suggesting that pleiotropism and or tight linkage of different traits could be the possible reason for the congruence of several QTL. The many QTL detected by the same marker interval across environments indicate that QTL for most traits are stable and not essentially affected by environmental factors.

Unconditional and Conditional QTL Mapping for Tiller Numbers at Various Stages with Single Segment Substitution Lines in Rice (Oryza sativa L.)

Abstract Tiller is one of the most important agronomic traits which influences quantity and quality of effective panicles and finally influences yield in rice. It is important to understand “static” and “dynamic” information of the QTLs for tillers in rice. This work was the first time to simultaneously map unconditional and conditional QTLs for tiller numbers at various stages by using single segment substitution lines in rice. Fourteen QTLs for tiller number, distributing on the corresponding substitution segments of chromosomes 1, 2, 3, 4, 6, 7 and 8 were detected. Both the number and the effect of the QTLs for tiller number were various at different stages, from 6 to 9 in the number and from 1.49 to 3.49 in the effect, respectively. Tiller number QTLs expressed in a time order, mainly detected at three stages of 0–7 d, 14–21 d and 35–42 d after transplanting with 6 positive, 9 random and 6 negative expressing QTLs, respectively. Each of the QTLs expressed one time at least during the whole duration of rice. The tiller number at a specific stage was determined by sum of QTL effects estimated by the unconditional method, while the increasing or decreasing number in a given time interval was controlled by the total of QTL effects estimated by the conditional method. These results demonstrated that it is highly effective and accurate for mapping of the QTLs by using single segment substitution lines and the conditional analysis methodology.

Overcoming inter-subspecific hybrid sterility in rice by developing indica -compatible japonica lines

Rice (Oryza sativa L.) is an important staple crop. The exploitation of the great heterosis that exists in the inter-subspecific crosses between the indica and japonica rice has long been considered as a promising way to increase the yield potential. However, the male and female sterility frequently occurred in the inter-subspecific hybrids hampered the utilization of the heterosis. Here we report that the inter-subspecific hybrid sterility in rice is mainly affected by the genes at Sb, Sc, Sd and Se loci for F1 male sterility and the gene at S5 locus for F1 female sterility. The indica-compatible japonica lines (ICJLs) developed by pyramiding the indica allele (S-i) at Sb, Sc, Sd and Se loci and the neutral allele (S-n) at S5 locus in japonica genetic background through marker-assisted selection are compatible with indica rice in pollen fertility and in spikelet fertility. These results showed a great promise of overcoming the inter-subspecific hybrid sterility and exploiting the heterosis by developing ICJLs.

Detection and characterization of epistasis between QTLs on plant height in rice using single segment substitution lines

Hua-jing-xian 74 and its 12 single segment substitution lines (SSSLs) in rice were used as crossing parents to construct a half diallel crossing population. A total number of 91 materials were grown under three planting densities. By analysis of average plant height (PH) over all environments 10 SSSLs were detected with significant additives and 6 SSSLs with significant dominances. These SSSLs were further tested under different densities respectively, indicating that some of single locus effects were sensitive to densities and the conditions under the density of 16.7 cm × 16.7 cm maybe inhibited the expressing of these PH QTLs. Qualitative and quantitative analyses of each four participating genotypes indicated that digenic interactions among these QTLs were prevalent. Of 66 tested interactions, about 42.4% were epistatic (P < 5%). Although some QTLs hadn’t single locus effects, they were possible to form digenic interactions. A significant finding was that the detected epistases were mostly negative. Additionally, these epistases were also found being sensitive to planting densities, the conditions under the density of 10 cm × 16.7 cm perhaps promoted the expressing of epistatic interactions among PH QTLs.

Analysis of QTLs on heading date based on single segment substitution lines in rice ( Oryza Sativa L.)

Single segment substitution lines (SSSLs) have been confirmed to be powerful tools to perform quantitative trait locus (QTL) analysis. This study illuminated the process and methods of QTL analysis with SSSLs on heading date (HD) in rice. QTL identification under two cropping seasons revealed 98 of 202 SSSLs associated with HD. A total of 22 QTLs were positioned in relative narrow regions on chromosomes by mrMLM.GUI software. QTL qHd3-1 was precisely positioned at 4.4 cM on chromosome 3 by a secondary F2 population. Through SSSL pyramiding, double segment substitution lines were constructed and used to analyze epistatic interactions of digenic loci. Epistatic effects for three pairs of QTLs were estimated, indicating the interactions of QTL qHd3-1 with other QTLs detected and the role to enhance the expression of early ripening or restraining of late flowering QTLs. Additionally, analysis of QTL in different environments provided information about the stability of HD QTLs. This type of research points out the way to excavate favorable genes for design breeding.

Genome-wide transcriptome profiling provides insights into panicle development of rice (Oryza sativa L.).

Panicle architecture is an important component of agronomic trait in rice, which is also a key ingredient that could influence yield and quality of rice. In the panicle growth and development process, there are a series of complicated molecular and cellular events which are regulated by many interlinking genes. In this study, to explore the potential mechanism and identify genes and pathways involved in the formation of rice panicle, we compared the transcriptional profile of rice panicles (NIL-GW8 and NIL-gw8Amol) at three different stages of panicle development: In5 (formation of higher-order branches), In6 (differentiation of glumes) and In7 (differentiation of floral organs). A range of 40.5 to 54.1 million clean reads was aligned to 31,209 genes in our RNA-Seq analysis. In addition, we investigated transcriptomic changes between the two rice lines during different stages. A total of 726, 1121 and 2584 differentially expressed genes (DEGs) were identified at stages 1, 2 and 3, respectively. Based on an impact analysis of the DEGs, we hypothesize that MADS-box gene family, cytochrome P450 (CYP) and pentatricopeptide repeat (PPR) protein and various transcription factors may be involved in regulation of panicle development. Further, we also explored the functional properties of DEGs by gene ontology analysis, and the results showed that different numbers of DEGs genes were associated with 53 GO groups. In KEGG pathway enrichment analysis, many DEGs related to biosynthesis of secondary metabolites and plant hormone signal transduction, suggesting their important roles during panicle development. This study provides the first examination of changes in gene expression between different panicle development stages in rice. Our results of transcriptomic characterization provide important information to elucidate the complex molecular and cellular events about the panicle formation in rice or other cereal crops. Also, the findings will be helpful for the further identification of the genes related to panicle development.