Utilization of natural alleles for heat adaptability QTLs at the flowering stage in rice.

BACKGROUND: Heat stress threatens rice yield and quality at flowering stage. In this study, average relative seed setting rate under heat stress (RHSR) and genotypes of 284 varieties were used for a genome-wide association study. RESULTS: We identified eight and six QTLs distributed on chromosomes 1, 3, 4, 5, 7 and 12 in the full population and indica, respectively. qHTT4.2 was detected in both the full population and indica as an overlapping QTL. RHSR was positively correlated with the accumulation of heat-tolerant superior alleles (SA), and indica accession contained at least two heat-tolerant SA with average RHSR greater than 43%, meeting the needs of stable production and heat-tolerant QTLs were offer yield basic for chalkiness degree, amylose content, gel consistency and gelatinization temperature. Chalkiness degree, amylose content, and gelatinization temperature under heat stress increased with accumulation of heat-tolerant SA. Gel consistency under heat stress decreased with polymerization of heat-tolerant SA. The study revealed qHTT4.2 as a stable heat-tolerant QTL that can be used for breeding that was detected in the full population and indica. And the grain quality of qHTT4.2-haplotype1 (Hap1) with chalk5, wx, and alk was better than that of qHTT4.2-Hap1 with CHALK5, WX, and ALK. Twelve putative candidate genes were identified for qHTT4.2 that enhance RHSR based on gene expression data and these genes were validated in two groups. Candidate genes LOC_Os04g52830 and LOC_Os04g52870 were induced by high temperature. CONCLUSIONS: Our findings identify strong heat-tolerant cultivars and heat-tolerant QTLs with great potential value to improve rice tolerance to heat stress, and suggest a strategy for the breeding of yield-balance-quality heat-tolerant crop varieties.

OrMKK3 Influences Morphology and Grain Size in Rice.

Although morphology and grain size are important to rice growth and yield, the identity of abundant natural allelic variations that determine agronomically important differences in crops is unknown. Here, we characterized the function of mitogen-activated protein kinase 3 from Oryza officinalis Wall. ex Watt encoded by OrMKK3. Different alternative splicing variants occurred in OrMKK3. Green fluorescent protein (GFP)-OrMKK3 fusion proteins localized to the cell membrane and nuclei of rice protoplasts. Overexpression of OrMKK3 influenced the expression levels of the grain size-related genes SMG1, GW8, GL3, GW2, and DEP3. Phylogenetic analysis showed that OrMKK3 is well conserved in plants while showing large amounts of variation between indica, japonica, and wild rice. In addition, OrMKK3 slightly influenced brassinosteroid (BR) responses and the expression levels of BR-related genes. Our findings thus identify a new gene, OrMKK3, influencing morphology and grain size and that represents a possible link between mitogen-activated protein kinase and BR response pathways in grain growth. Supplementary Information: The online version contains supplementary material available at 10.1007/s12374-020-09290-2.

QTL mapping and identification of candidate genes for cold tolerance at the germination stage in wild rice.

BACKGROUND: Cold damage stress significantly affects rice growth (germination and seedling) and causes serious losses in yield in temperate and high-altitude areas around the globe. OBJECTIVE: This study aimed to explore the cold tolerance (CT) locus of rice and create new cold-tolerant germplasm. We constructed a chromosome segment substitution line (CSSL) with strong CT and fine mapped quantitative trait loci (QTLs) associated with CT by performing the whole-genome resequencing of CSSL with phenotypes under cold treatment. METHODS: A chromosome CSSL, including 271 lines from a cross between the cold-tolerant wild rice Y11 (Oryza rufipogon Griff.) and the cold-sensitive rice variety GH998, was developed to map QTLs conferring CT at the germination stage. The whole-genome resequencing was performed on CSSL for mapping QTLs of associated with CT at the germination stage. RESULTS: A high-density linkage map of the CSSLs was developed using the whole-genome resequencing of 1484 bins. The QTL analysis using 615,466 single-nucleotide polymorphisms (SNPs) led to the identification of 2 QTLs related to germination rate at low-temperature on chromosome 8 (qCTG-8) and chromosome 11 (qCTG-11). The qCTG-8 and qCTG-11 explained 14.55% and 14.31% of the total phenotypic variation, respectively. We narrowed down qCTG-8 and qCTG-11 to 195.5 and 78.83-kb regions, respectively. The expression patterns of important candidate genes in different tissues, and of RNA-sequencing (RNA-seq) in CSSLs, were identified based on gene sequences in qCTG-8 and qCTG-11 cold-induced expression analysis. LOC_Os08g01120 and LOC_Os08g01390 were identified as candidate genes in qCTG-8, and LOC_Os11g32880 was identified as a candidate gene in qCTG-11. CONCLUSIONS: This study demonstrated a general method that could be used to identify useful loci and genes in wild rice and aid in the future cloning of candidate genes of qCTG-8 and qCTG-11. The CSSLs with strong CT were supported for breeding cold-tolerant rice varieties.

Systematic Analysis of NB-ARC Gene Family in Rice and Functional Characterization of GNP12.

The NB-ARC (nucleotide-binding adaptor shared by APAF-1, R proteins, and CED-4) gene family plays a critical role in plant development. However, our understanding of the mechanisms of how NB-ARC genes regulate plant development in the plant panicle is still limited. Here, we subjected 258 NB-ARC genes in rice to genome-wide analysis to characterize their structure, function, and expression patterns. The NB-ARC genes were classified into three major groups, and group II included nine subgroups. Evolutionary analysis of NB-ARC genes in a dicotyledon plant (Arabidopsis thaliana) and two monocotyledonous plants (Oryza sativa L. and Triticum aestivum) indicated that homologous genome segments were conserved in monocotyledons and subjected to weak positive selective pressure during evolution. Dispersed and proximal replication events were detected. Expression analysis showed expression of most NB-ARC genes in roots, panicles, and leaves, and regulation at the panicle development stage in rice Ce253. The GNP12 gene encodes RGH1A protein, which regulates rice yield according to panicle length, grain number of panicle, and grain length, with eight major haplotypes. Most members of NB-ARC protein family are predicted to contain P-loop conserved domains and localize on the membrane. The results of this study will provide insight into the characteristics and evolution of NB-ARC family and suggest that GNP12 positively regulates panicle development.

Cis-cinnamic acid-enhanced 1 gene plays a role in regulation of Arabidopsis bolting.

Cis-cinnamic acid (CA) is one of many cis-phenylpropanoids found in both monocots and dicots. It is produced in planta via sunlight-mediated isomerization of trans-cinnamic acid. This pair of isomers plays a differential role in regulation of plant growth. A functional proteomics approach has been adopted to identify genes of cis/trans-CA mixture-enhanced expression. Out of 1,241 proteins identified by mass spectrometry, 32 were CA-enhanced and 13 repressed. Further analysis with the molecular biology approach revealed 2 cis-CA (Z usammen-CA)-E nhanced genes, named ZCE1 and ZCE2, which encode members of the major latex protein-like (MLPL) gene family. The transcript accumulation of both genes is positively correlated with the amount of cis-CA applied externally, ranging from 1 to 100 µM. ZCE1 transcript accumulation is enhanced largely by cis-CA and slightly by other cis-phenylpropanoids. Treatment of several well-characterized plant growth regulator perception-deficient mutants with cis-CA is able to promote ZCE1 transcript accumulation, suggestive of distinct signaling pathways regulating cis-CA response. The zce1 loss-of-function mutant produced via the RNA-interference technique produces an earlier bolting phenotype in Arabidopsis, suggesting that ZCE1 plays a role in promoting vegetative growth and delay flowering.

The panorama of physiological responses and gene expression of whole plant of maize inbred line YQ7-96 at the three-leaf stage under water deficit and re-watering.

Changes in water potential, growth elongation, photosynthesis of three-leaf-old seedlings of maize inbred line YQ7-96 under water deficit (WD) for 0.5, 1 and 2 h and re-watering (RW) for 24 h were characterized. Gene expression was analyzed using cDNA microarray covering 11,855 maize unigenes. As for whole maize plant, the expression of WD-regulated genes was characterized by up-regulation. The expression of WD-regulated genes was categorized into eight different patterns, respectively, in leaves and roots. Newly found and WD-affected cellular processes were metabolic process, amino acid and derivative metabolic process and cell death. A great number of the analyzed genes were found to be regulated specifically by RW and commonly by both WD and RW, respectively, in leaves. It is therefore concluded that (1) whole maize plant tolerance to WD, as well as growth recovery from WD, depends at least in part on transcriptional coordination between leaves and roots; (2) WD exerts effects on the maize, especially on basal metabolism; (3) WD could probably affect CO(2) uptake and partitioning, and transport of fixed carbons; (4) WD could likely influence nuclear activity and genome stability; and (5) maize growth recovery from WD is likely involved in some specific signaling pathways related to RW-specific responsive genes.

Comparative profiles of gene expression in leaves and roots of maize seedlings under conditions of salt stress and the removal of salt stress.

We studied the transcriptional profiles of leaves and roots of three-leaf stage seedlings of the maize inbred line YQ7-96 under conditions of salt stress (100 mM NaCl) and removal of salt stress (RSS). A total of 296 genes were regulated specifically by the stress, of which 206 were specific to leaves and 90 were specific to roots. Stress-regulated genes were classified into eight and seven expression patterns for leaves and roots, respectively. There were 60 genes which were regulated specifically by RSS, 27 of which were specific to leaves and 33 specific to roots. No genes were found to be co-regulated in tissues and to be regulated commonly by the stress and RSS. It can be concluded that (i) at the early stage of the stress, transcriptional responses are directed at water deficit in maize leaves but at both water deficit and Na+ accumulation in roots; (ii) at the later stage, the responses in leaves and roots result from dual effects of both water deficit and Na+ accumulation; (iii) the polyamine metabolic pathway is an important linker for the co-ordination between leaves and roots to accomplish the tolerance of the whole maize plant to the stress; (iv) the stress can lead to genomic restructuring and nuclear transport in maize; (v) maize leaves are distinct from roots in terms of molecular mechanisms for responses to and growth recovery from the stress; and (vi) mechanisms for the maize responses to the stress differ from those for their growth recovery during RSS.