Genetic dissection of top three leaf traits in rice using progenies from a japonica × indica cross

Mapping and Validation of Quantitative Trait Loci on Yield-Related Traits Using Bi-Parental Recombinant Inbred Lines and Reciprocal Single-Segment Substitution Lines in Rice (Oryza sativa L.)

Yield-related traits have higher heritability and lower genotype-by-environment interaction, making them more suitable for genetic studies in comparison with the yield per se. Different populations have been developed and employed in QTL mapping; however, the use of reciprocal SSSLs is limited. In this study, three kinds of bi-parental populations were used to investigate the stable and novel QTLs on six yield-related traits, i.e., plant height (PH), heading date (HD), thousand-grain weight (TGW), effective tiller number (ETN), number of spikelets per panicle (NSP), and seed set percentage (SS). Two parental lines, i.e., japonica Asominori and indica IR24, their recombinant inbred lines (RILs), and reciprocal single-segment substitution lines (SSSLs), i.e., AIS and IAS, were genotyped by SSR markers and phenotyped in four environments with two replications. Broad-sense heritability of the six traits ranged from 0.67 to 0.94, indicating their suitability for QTL mapping. In the RIL population, 18 stable QTLs were identified for the six traits, 4 for PH, 6 for HD, 5 for TGW, and 1 each for ETN, NSP, and SS. Eight of them were validated by the AIS and IAS populations. The results indicated that the allele from IR24 increased PH, and the alternative allele from Asominori reduced PH at qPH3-1. AIS18, AIS19, and AIS20 were identified to be the donor parents which can be used to increase PH in japonica rice; on the other hand, IAS14 and IAS15 can be used to reduce PH in indica rice. The allele from IR24 delayed HD, and the alternative allele reduced HD at qHD3-1. AIS14 and AIS15 were identified to be the donor parents which can be used to delay HD in japonica rice; IAS13 and IAS14 can be used to reduce HD in indica rice. Reciprocal SSSLs not only are the ideal genetic materials for QTL validation, but also provide the opportunity for fine mapping and gene cloning of the validated QTLs.

Identification and Transcriptome Analysis of a Novel Allelic Mutant of NAL1 in Rice

Leaf morphology is a crucial aspect of plant architecture, yet the molecular mechanisms underlying leaf development remain incompletely understood. In this study, a narrow leaf mutant, m625, was identified in rice (Oryza sativa L.), exhibiting pleiotropic developmental defects. Pigment measurement revealed reduced levels of photochromic pigments in m625. Cytological analysis demonstrated that the m625 gene affected vascular patterns and cell division. Specifically, the narrowing of the leaf was attributed to a decrease in small vein number, shorter vein spacing, and an abnormal V-shaped arrangement of bulliform cells, while the thickening was caused by longer leaf veins, thicker mesophyll cells, and an increased number of parenchyma cell layers. The dwarf stature and thickened internode were primarily due to shortened internodes and an increase in cell layers, respectively. Positional cloning and complementation assays indicated that the m625 gene is a novel allele of NAL1. In the m625 mutant, a nucleotide deletion at position 1103 in the coding sequence of NAL1 led to premature termination of protein translation. Further RNA-Seq and qRT-PCR analyses revealed that the m625 gene significantly impacted regulatory pathways related to IAA and ABA signal transduction, photosynthesis, and lignin biosynthesis. Moreover, the m625 mutant displayed thinner sclerenchyma and cell walls in both the leaf and stem, particularly showing reduced lignified cell walls in the midrib of the leaf. In conclusion, our study suggests that NAL1, in addition to its known roles in IAA transport and leaf photosynthesis, may also participate in ABA signal transduction, as well as regulate secondary cell wall formation and sclerenchyma thickness through lignification.

Exploration of chlorophyll fluorescence characteristics gene regulatory in rice (Oryza sativa L.): a genome-wide association study

Chlorophyll content and fluorescence parameters are crucial indicators to evaluate the light use efficiency in rice; however, the correlations among these parameters and the underlying genetic mechanisms remain poorly understood. Here, to clarify these issues, we conducted a genome-wide association study (GWAS) on 225 rice accessions. In the phenotypic and Mendelian randomization (MR) analysis, a weak negative correlation was observed between the chlorophyll content and actual quantum yield of photosystem II (Φ I I ). The phenotypic diversity observed in SPAD, N P Q t , Φ N P Q , and F v / F m among accessions was affected by genetic background. Furthermore, the GWAS identified 78 SNPs and 17 candidate genes significantly associated with SPAD, N P Q t , Φ I I , Φ N P Q , q L and q P . Combining GWAS on 225 rice accessions with transcriptome analysis of two varieties exhibiting distinct fluorescence characteristics revealed two potential candidate genes (Os03g0583000 from Φ I I & q P traits and Os06g0587200 from N P Q t trait), which are respectively associated with peroxisomes, and protein kinase catalytic domains might involve in regulating the chlorophyll content and chlorophyll fluorescence. This study provides novel insights into the correlation among chlorophyll content and fluorescence parameters and the genetic mechanisms in rice, and offers valuable information for the breeding of rice with enhanced photosynthetic efficiency.

Identification of quantitative trait loci for important agronomic traits using chromosome segment substitution lines from a japonica × indica cross in rice

Asian cultivated rice (Oryza sativa L.) has two subspecies, indica and japonica, which display clear differences in yield-related traits and environmental adaptation. Here, we developed a set of chromosome segment substitution lines (CSSLs) from an advanced backcross between japonica variety C418, as the recipient, and indica variety IR24, as the donor. Through evaluating the genotypes and phenotypes of 181 CSSLs, a total of 85 quantitative trait loci (QTLs) for 14 yield-related traits were detected, with individual QTLs explaining from 6.2 to 42.9% of the phenotypic variation. Moreover, twenty-six of these QTLs could be detected in the two trial sites (Beijing and Hainan). Among these loci, the QTLs for flag leaf width and effective tiller number, qFLW4.2 and qETN4.2, were delimited to an approximately 256-kb interval on chromosome 4. Through a comparison of nucleotide sequences and expression levels in "C418" and the CSSL CR31 containing qFLW4.2 and qETN4.2, we found that the NAL1 (LOC_Os04g52479) gene was the candidate gene for qFLW4.2 and qETN4.2. Our results show that CSSLs are powerful tools for identifying and fine-mapping QTLs, while the novel QTLs identified in this study will also provide new genetic resources for rice improvement.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-022-01343-3.

Genetic dissection of rhizome yield-related traits in Nelumbo nucifera through genetic linkage map construction and QTL mapping

Lotus (Nelumbo nucifera) is a perennial aquatic plant with great value in ornamentation, nutrition, and medicine. Being a storage organ, lotus rhizome is not only used for vegetative reproduction, but also as a popular vegetable in Southeast Asia. Rhizome development, especially enlargement, largely determines its yield and hence becomes one of the major concerns in rhizome lotus breeding and cultivation. To obtain the genetic characteristic of this trait, and discover markers or genes associated with this trait, an F₂ population was generated by crossing between temperate and tropical cultivars with contrasting rhizome enlargement. Based on this F₂ population and Genotyping-by-Sequencing (GBS) technique, a genetic map was constructed with 1475 bin markers containing 12,113 SNP markers. Six traits associated with rhizome yield were observed over 3 years. Quantitative trait locus (QTL) mapping analysis identified 22 QTLs that are associated with at least one of these traits, among which 9 were linked with 3 different intervals. Comparison of the genes located in these three intervals with our previous transcriptomic data showed that light and phytohormone signaling might contribute to the development and enlargement of lotus rhizome. The QTLs obtained here could also be used for marker-assisted breeding of rhizome lotus.

Genetic Mapping with Background Control for Quantitative Trait Locus (QTL) in 8-Parental Pure-Line Populations

Multiparental advanced generation intercross (MAGIC) populations provide abundant genetic variation for use in plant genetics and breeding. In this study, we developed a method for quantitative trait locus (QTL) detection in pure-line populations derived from 8-way crosses, based on the principles of inclusive composite interval mapping (ICIM). We considered 8 parents carrying different alleles with different effects. To estimate the 8 genotypic effects, 1-locus genetic model was first built. Then, an orthogonal linear model of phenotypes against marker variables was established to explain genetic effects of the locus. The linear model was estimated by stepwise regression and finally used for phenotype adjustment and background genetic variation control in QTL mapping. Simulation studies using 3 genetic models demonstrated that the proposed method had higher detection power, lower false discovery rate (FDR), and unbiased estimation of QTL locations compared with other methods. Marginal bias was observed in the estimation of QTL effects. An 8-parental recombinant inbred line (RIL) population previously reported in cowpea and analyzed by interval mapping (IM) was reanalyzed by ICIM and genome-wide association mapping implemented in software FarmCPU. The results indicated that ICIM identified more QTLs explaining more phenotypic variation than did IM; ICIM provided more information on the detected QTL than did FarmCPU; and most QTLs identified by IM and FarmCPU were also detected by ICIM.

Genome-wide transcriptome profile of rice hybrids with and without Oryza rufipogon introgression reveals candidate genes for yield

In this study, we compared genome-wide transcriptome profile of two rice hybrids, one with (test hybrid IR79156A/IL50-13) and the other without (control hybrid IR79156A/KMR3) O. rufipogon introgressions to identify candidate genes related to grain yield in the test hybrid. IL50-13 (Chinsurah Nona2 IET21943) the male parent (restorer) used in the test hybrid, is an elite BC₄F₈ introgression line of KMR3 with O. rufipogon introgressions. We identified 2798 differentially expressed genes (DEGs) in flag leaf and 3706 DEGs in panicle. Overall, 78 DEGs were within the major yield QTL qyld2.1 and 25 within minor QTL qyld8.2. The DEGs were significantly (p < 0.05) enriched in starch synthesis, phenyl propanoid pathway, ubiquitin degradation and phytohormone related pathways in test hybrid compared to control hybrid. Sequence analysis of 136 DEGs from KMR3 and IL50-13 revealed 19 DEGs with SNP/InDel variations. Of the 19 DEGs only 6 showed both SNP and InDel variations in exon regions. Of these, two DEGs within qyld2.1, Phenylalanine ammonia- lyase (PAL) (Os02t0626400-01, OsPAL2) showed 184 SNPs and 11 InDel variations and Similar to phenylalanine ammonia- lyase (Os02t0627100-01, OsPAL4) showed 205 SNPs and 13 InDel variations. Both PAL genes within qyld2.1 and derived from O. rufipogon are high priority candidate genes for increasing grain yield in rice.

Construction of a High-Density Genetic Map Based on SLAF Markers and QTL Analysis of Leaf Size in Rice

Leaf shape is an important agronomic trait for constructing an ideal plant type in rice, and high-density genetic map is facilitative in improving accuracy and efficiency for quantitative trait loci (QTL) analysis of leaf trait. In this study, a high-density genetic map contained 10,760 specific length amplified fragment sequencing (SLAF) markers was established based on 149 recombinant inbred lines (RILs) derived from the cross between Rekuangeng (RKG) and Taizhong1 (TN1), which exhibited 1,613.59 cM map distance with an average interval of 0.17 cM. A total of 24 QTLs were detected and explained the phenotypic variance ranged from 9% to 33.8% related to the leaf morphology across two areas. Among them, one uncloned major QTL qTLLW1 (qTLL1 and qTLLW1) involved in regulating leaf length and leaf width with max 33.8% and 22.5% phenotypic variance respectively was located on chromosome 1, and another major locus qTLW4 affecting leaf width accounted for max 25.3% phenotypic variance was mapped on chromosome 4. Fine mapping and qRT-PCR expression analysis indicated that qTLW4 may be allelic to NAL1 (Narrow leaf 1) gene.

Genetic Mapping and Validation of Quantitative Trait Loci (QTL) for the Grain Appearance and Quality Traits in Rice (Oryza sativa L.) by Using Recombinant Inbred Line (RIL) Population

Rice grain shape and nutritional quality traits have high economic value for commercial production of rice and largely determine the market price, besides influencing the global food demand for high-quality rice. In order to understand the genetic components of grain appearance traits in paddy, brown, and head rice, 15 traits were evaluated by using 157 recombinant inbred lines (RILs) derived from a cross between two Iranian rice cultivars Ali-Kazemi (A) and Kadous (K). A significant variation was observed and showed transgressive segregation among the RILs. Correlations between the visual appearances of grain traits were studied. A linkage map with 65 polymorphic SSR markers was constructed, which covered 1517.32 cM of the rice genome. A total of seven QTLs were identified on four chromosomes, 1, 6, 9, and 12, associated with four traits, which are explained by the total phenotypic variation of 44.27% and LOD score of 32.77 in 2014 and 2015, respectively. Among these, four QTLs for two traits were consistently flanked by RM23904 and RM24432 on chromosome 9. Single QTL for head grain length (HGL) expressed in both the years on chromosomes 1 and 9. A major QTL for seed weight was detected on chromosome 9, which explained 10.18% of the phenotypic variation. The additive effect of all the QTLs was positively contributed by Ali-Kazemi allele, except one QTL on chromosome 6 (qBGL_6) that showed a negative additive effect being contributed by the Kadous allele. The study also validated the identified QTLs with the polymorphic SSR markers that were previously reported. Novel QTLs were identified on chromosomes 6 and 9, and many of the polymorphic markers were found to be associated with milling processing of grain quality, cooking, and nutraceutical properties of rice by extensive literature and database analysis. Therefore, these validated QTLs and marker information could be utilized in the marker-assisted selection to improve grain appearance and nutritional grain quality traits in rice.