Key message A minor QTL for grain weight in rice, qTGW1.2b, was fine-mapped. Its casual gene OsVQ4 was confirmed through CRISPR/Cas9-targeted mutagenesis, exhibiting an effect that was larger than the original QTL effect. Abstract The CRISPR/Cas system exhibits a great potential for rice improvement, but the application was severely hindered due to insufficient target genes, especial the lack of validated genes underlying quantitative trait loci having small effects. In this study, a minor QTL for grain weight, qTGW1.2b, was fine-mapped into a 44.0 kb region using seven sets of near isogenic lines (NILs) developed from the indica rice cross (Zhenshan 97)3/Milyang 46, followed by validation of the causal gene using CRISPR/Cas9-targeted mutagenesis. In the NIL populations, 1000-grain weight of the Zhenshan 97 homozygous lines decreased by 0.9–2.0% compared with the Milyang 46 homozygous lines. A gene encoding VQ-motif protein, OsVQ4, was identified as the candidate gene based on parental sequence differences. The effect of OsVQ4 was confirmed by creating CRISPR/Cas9 knockout lines, whose 1000-grain weight decreased by 2.8–9.8% compared with the wild-type transgenic line and the recipient. These results indicate that applying genome editing system could create novel alleles with large phenotypic variation at minor QTLs, which is an effective way to validate causal genes of minor QTLs. Our study establishes a strategy for cloning minor QTLs, which could also be used to identify a large number of potential target genes for the application of CRISPR/Cas system.

No abstract

Chlorophyll, one of the major chloroplast components for photosynthesis, has a positive relationship with the photosynthetic rate. The chlorophyll content is an important assessment parameter in agronomy and plant biology research. This study was conducted to evaluate the natural variation in the chlorophyll content and to determine the differential response of the chlorophyll concentration to dark treatment in a natural population containing 139 maize inbreds. A five-fold higher chlorophyll concentration was measured in the light compared with the dark. Meanwhile, the wide variation in the chlorophyll concentration showed the differential response of the natural maize population to dark. Finally, we identified some inbreds that were highly sensitive to the dark with more than 70% difference between the light and dark treatment, such as Dan598, Zheng29, Zheng35, DH29, and R08, as well as some inbreds that had lower sensitivity to the dark, with less than 35% difference in the chlorophyll content between the light and dark treatment, such as Chuan48-2, 4F1, 303WX, 9642, and LY042.

Grain size is the major determinant of grain weight, and a trait having an important role in grain quality. It is controlled by several major quantitative trait loci (QTL) and many minor QTL. Identification of QTL for grain size is important for understanding the genetic and molecular network regulating grain size in rice. Following previous identification of QTL for grain weight and size using an F 2:3 family derived from the indica rice cross Teqing/IRBB52, one QTL, qTGW5 having significant effects on grain length and weight was targeted for validation, dissection and fine-mapping. Firstly, the effect of qTGW5 was validated using two near-isogenic line (NIL)-F 2 populations. Then, qTGW5 was dissected into two closely linked QTL using four NIL populations. One of them, qGL5.1, having significant effects on grain length, width and weight, was located within an 1896.4-kb region. The other one, qGL5.2 controlling grain length, was further delimited into a 68.8-kb region using seven NIL-F 2 populations. Six annotated genes were found in the qGL5.2 region, of which five showed nucleotide polymorphisms between the two parental lines. Additionally, three of the six annotated genes showed significant expression differences between NIL Teqing and NIL IRBB52 in young panicles using qRT-PCR. The results will facilitate cloning the minor QTL and understanding the genetic architecture for grain size in rice.

No abstract

Chlorophyll is an important pigment that is involved in the process of photosynthesis in plants and some algae. Different photoperiods and chlorophyll contents affect grain yield and plant health. In the present study, one recombinant inbred line (RIL) population constructed by using Zong3 and Yu87-1 was used for quantitative genetics analysis of chlorophyll content before and after dark treatment at the seedling stage. Chlorophyll index of the first and second leaves of six plants from each line were measured with SPAD-502 before and after dark treatment. A total of 19 putative quantitative trait loci (QTLs) were identified with each accounted for 6.87-15.9% of the observed phenotypic variation. Moreover, eight major putative QTLs that explained more than 10% of the observed phenotypic variation were identified. In addition, one QTL located on chromosome 3, which affected DF (SPAD value at the first leaf after dark treatment) and LF (SPAD value at the first leaf before dark treatment) was co-localized with a candidate gene (GRMZM2G170013 translated into chlorophyll b reductase) of the chlorophyll pathway. These results help better understand the genetic background of chlorophyll during dark-induced senescence and photoperiodic variations.

Background: Most agronomical traits of crops are complex traits controlled by several major quantitative trait locus (QTL) and many minor QTL. Grain size determines grain weight and influences rice appearance quality. Identification of minor QTL is important for understanding the genetic and molecular network regulating grain size in rice. Following previous identification of QTL for grain weight and size using populations derived from the Teqing/IRBB52 indica rice cross, one QTL, qTGW5/qGL5 having significant effects on grain weight and length, was targeted for validation, dissection and fine-mapping.Result: Firstly, the effect of qTGW5/qGL5 was validated using two near isogenic line (NIL) F2 populations. Then, qTGW5/qGL5 was dissected into two closely linked QTL for grain size using four sets of NILs with sequential segregating regions. One of them, qTGW5 with the IRBB52 alleles increased grain weight, length and width with the same allelic direction, was located within an 1896.4-kb region flanked by RM18865 and Fi25273. The other one, qGL5 controlling grain length, was further delimited into a 68.8-kb region using seven NIL-F2 populations. Six annotated genes were found in the qGL5 region, of which five showed nucleotide polymorphisms between the two parental lines. In three of the six annotated genes, significant expression differences were detected between qGL5-NILs.Conclusions: Two closely-linked QTL having small effects for grain size in rice were separated using NIL-derived populations. One of them, qGL5 was fine-mapped into a 68.8-kb region containing six annotated genes. Our work lays a foundation for cloning minor QTL for grain size and offers potential targets for marker-assisted breeding in rice.