Intron Retention Fine-Tunes the Resistance of the Rice Mutant pls4 to Rice Sheath Blight(Rhizotonia solani AG I.1a)

OsPLS4 encodes aβ-ketoacyl carrier protein reductase(KAR).The role of OsPLS4 in rice sheath blight(Rhizoctonia solani)remains unclear.Our preliminary studies showed that premature leaf senescence mutants(pls4)were highly susceptive to sheath blight in the early stage of rice development.To explore the role of this gene in the development of rice sheath blight,the transcriptome profiles of the rice pls4 mutant and wild type were compared by RNA-seq.The results revealed 2,569 differentially expressed genes(DEGs).The down-regulated genes were significantly enriched in the defense response-related biological processes.These down-regulated genes included the chitinase genes and WRKY genes,which were significantly changed in pls4 mutants.Furthermore,467 genes induced significant alternative splicing(AS)events.Among them,intron retention(IR)affected gene expression levels and functions of the vitamin B6(VB6)metabolism pathway related to sheath blight.This result suggests that IR plays an important role in the sheath blight resistance of mutant pls4.Together,these results indicate that pls4 could be involved in the biological process of sheath blight via DEGs and the fine-tuning of IR.The present study provides a molecular basis for further investigation of the resistance of rice to sheath blight.

Natural variation of an autophagy-family gene among rice subspecies affects grain size and weight

Elucidating the genetic basis of natural variation in grain size and weight among rice varieties can help breeders develop high-yielding varieties.We identified a novel gene,GW3a(Grain Weight 3a)(LOC_Os03g27350),that affects rice grain size and weight.gw3a mutants showed higher total starch content and dry matter accumulation than the wild type(WT),Nipponbare,suggesting that GW3a negatively regulates grain size and weight.Moreover,our study found that GW3a interacted with OsATG8 by cleaving it,suggesting that GW3a may be involved in the assembly of autophagosomes and starch degradation in plants.The haplotype analysis of GW3a showed functional differences between indica and japonica rice.Taken together,we conclude that GW3a is expressed in the autophagosome pathway regulating starch metabolism in rice,affecting yield-related traits,such as grain size,grain weight and thousand grain weight(TGW).Our findings also shed new light on autophagy-mediated yield trait regulation,proposing a possible strategy for the genetic improvement of high-yield germplasm in rice.

A Novel QTL qTGW3 Encodes the GSK3/ SHAGGY-Like Kinase OsGSK5/OsSK41 that Interacts with OsARF4 to Negatively Regulate Grain Size and Weight in Rice

Grain size and shape are important determinants of grain weight and yield in rice. Here, we report a new major quantitative trait locus （QTL）, qTGW3, that controls grain size and weight in rice. This locus, qTGW3, encodes OsSK41 （also known as OsGSK5）, a member of the GLYCOGEN SYNTHASE KINASE 3/SHAGGY-like family. Rice near-isogenic lines carrying the loss-of-function allele of OsSK41 have increased grain length and weight. We demonstrate that OsSK41 interacts with and phosphorylates AUXIN RESPONSE FACTOR 4 （OsARF4）. Co-expression of OsSK41 with OsARF4 increases the accumulation of OsARF4 in rice protoplasts. Loss of function of OsARF4 results in larger rice grains. RNA-sequencing analysis suggests that OsARF4 and OsSK41 repress the expression of a common set of downstream genes, including some auxin-responsive genes, during rice grain development. The loss-of-function form of OsSK41 at qTGW3 represents a rare allele that has not been extensively utilized in rice breeding. Suppression of OsSK41 function by either targeted gene editing or QTL pyramiding enhances rice grain size and weight. Thus, our study reveals the important role of OsSK41 in rice grain development and provides new candidate genes for genetic improvement of grain yield in rice and perhaps in other cereal crops.

A Kelch Motif-Containing Serine/Threonine Protein Phosphatase Determines the Large Grain QTL Trait in Rice

A thorough understanding of the genetic basis of rice grain traits is critical for the improvement of rice （Oryza sativa L.） varieties. In this study, we generated an F2 population by crossing the large-grain japonica cultivar CW23 with Peiai 64 （PA64）, an elite indica small-grain cultivar. Using QTL analysis, 17 QTLs for five grain traits were detected on four different chromosomes. Eight of the QTLs were newly-identified in this study. In particular, qGL3-1, a newly-identified grain length QTL with the highest LOD value and largest phenotypic variation, was fine-mapped to the 17 kb region of chromosome 3. A serine/threonine protein phosphatase gene encoding a repeat domain containing two Kelch motifs was identified as the unique candidate gene corresponding to this QTL. A comparison of PA64 and CW23 sequences revealed a single nucleotide substitution （C→A） at position 1092 in exon 10, resulting in replacement of Asp （D） in PA64 with Glu （E） in CW23 for the 364th amino acid. This variation is located at the D position of the conserved sequence motif AVLDT of the Kelch repeat. Genetic analysis of a near-isogenic line （NIL） for qGL3-1 revealed that the allele qGL3-1 from CW23 has an additive or partly dominant effect, and is suitable for use in molecular marker-assisted selection.

SUPEROXIDE DISMUTASE FAMILY GENES IN WATERMELON AND THEIR RESPONSES TO DIFFERENT ABIOTIC STRESSES

Superoxide dismutase(SOD)is an important enzyme in the antioxidant system of plants and plays a vital role in stress responses by maintaining the dynamic balance of reactive oxygen species(ROS)concentrations.Genome-wide analysis of the SOD gene family in various plant species has been conducted but little is known about this gene family in watermelon(Citrullus lanatus).Here,eight SOD genes were identified in the watermelon genome and are designated Cl CSD1-5,Cl FSD1-2 and Cl MSD according to their metal cofactors.Phylogenetic analysis shows that SOD proteins from various plant species can be classified into five groups and members in the same group possess the same metal cofactor and similar subcellular localizations.Expression analysis of the Cl SOD genes indicates that they had tissue-specific expression patterns with high expression in different tissues including the leaves,flowers and fruits.In addition,the expression of Cl SOD genes differed appreciably under salinity,drought and abscisic acid(ABA)treatments,indicating that they may be involved in ROS scavenging under different abiotic stresses via an ABA-dependent signaling pathway.These results lay the foundation for elucidating the function of Cl SOD genes in stress tolerance and fruit development in watermelon.

Genetic Analysis and Fine Mapping of a Novel Semidominant Dwarfing Gene LB4D in Rice

A dwarf mutant,designated LB4D,was obtained among the progeny of backcrosses to a wild rice introgression line.Genetic analysis of LB4D indicated that the dwarf phenotype was controlled by a single semidominant dwarfing gene,which was named LB4D.The mutants were categorized as dn-type dwarf mutants according to the pattern of internode reduction.In addition,gibberellin（GA） response tests showed that LB4D plants were neither deficient nor insensitive to GA.This study found that tiller formation by LB4D plants was decreased by 40%compared with the wild type,in contrast to other dominant dwarf mutants that have been identified,indicating that a different dwarfing mechanism might be involved in the LB4D dominant mutant.The reduction of plant height in F1 plants ranged from 27.9%to 38.1%in different genetic backgrounds,showing that LB4D exerted a stronger dominant dwarfing effect. Using large F2 and F3 populations derived from a cross between heterozygous LB4D and the japonica cultivar Nipponbare,the LB4D gene was localized to a 46 kb region between the markers Indel 4 and Indel G on the short arm of chromosome 11,and four predicted genes were identified as candidates in the target region.