Characterization of chromosome segment substitution lines reveals candidate genes associated with the nodule number in soybean

Soybean is one of the most important food crops worldwide.Like other legumes,soybean can form symbiotic relationships with Rhizobium species.Nitrogen fixation of soybean via its symbiosis with Rhizobium is pivotal for sustainable agriculture.Type Ⅲ effectors(T3Es)are essential regulators of the establishment of the symbiosis,and nodule number is a feature of nitrogen-affected nodulation.However,genes encoding T3Es at quantitative trait loci(QTLs)related to nodulation have rarely been identified.Chromosome segment substitution lines(CSSLs)have a common genetic background but only a few loci with heterogeneous genetic information;thus,they are suitable materials for identifying candidate genes at a target locus.In this study,a CSSL population was used to identify the QTLs related to nodule number in soybean.Single nucleotide polymorphism(SNP)markers and candidate genes within the QTLs interval were detected,and it was determined which genes showed differential expression between isolines.Four candidate genes(GmCDPK28,GmNAC1,GmbHLH,and GmERF5)linked to the SNPs were identified as being related to nodule traits and pivotal processes and pathways involved in symbiosis establishment.A candidate gene(GmERF5)encoding a transcription factor that may interact directly with the T3E NopAA was identified.The confirmed CSSLs with important segments and candidate genes identified in this study are valuable resources for further studies on the genetic network and T3Es involved in the signaling pathway that is essential for symbiosis establishment.

Genetic Variation Dissection of Rice Blast Resistance Using an Indica Population

Rice blast disease,caused by fungus pathogen Magnaporthe oryzae,is one of the most destructive diseases that impact rice farming.In the worldwide,rice harvests lose 10%to 30%of the total production because of blast infection,which is estimated to be enough for feeding 60 million people(Skamnioti and Gurr,2009).

Genetic and lipidomic analyses reveal the key role of lipid metabolism for cold tolerance in maize

Lipid remodeling is crucial for cold tolerance in plants.However,the precise alternations of lipidomics during cold responses remain elusive,especially in maize(Zea mays L.).In addition,the key genes responsible for cold tolerance in maize lipid metabolism have not been identified.Here,we integrate lipidomic,transcriptomic,and genetic analysis to determine the profile of lipid remodeling caused by cold stress.We find that the homeostasis of cellular lipid metabolism is essential for maintaining cold tolerance of maize.Also,we detect 210 lipid species belonging to 13 major classes,covering phospholipids,glycerides,glycolipids,and free fatty acids.Various lipid metabolites undergo specific and selective alterations in response to cold stress,especially mono-/di-unsaturated lysophosphatidic acid,lysophosphatidylcholine,phosphatidylcholine,and phosphatidylinositol,as well as polyunsaturated phosphatidic acid,monogalactosyldiacylglycerol,diacylglycerol,and triacylglycerol.In addition,we identify a subset of key enzymes,including ketoacyl-acyl-carrier protein synthase II(KAS II),acyl-carrier protein 2(ACP2),male sterility33(Ms33),and stearoyl-acyl-carrier protein desaturase 2(SAD2)involved in glycerolipid biosynthetic pathways are positive regulators of maize cold tolerance.These results reveal a comprehensive lipidomic profile during the cold response of maize and provide genetic resources for enhancing cold tolerance in crops.

Elite sd1 alleles in japonica rice and their breeding applications in northeast China

The Green Revolution gene sd1 has been used extensively in modern rice breeding,especially in indica cultivars.However,elite sd1 alleles and related germplasm resources used for japonica rice breeding have not been identified,and extensive efforts are needed for japonica rice breeding to obtain new dwarfing sources.Data from MBKbase-Rice revealed seven sd1 haplotypes in indica and four in japonica rice.Two new sd1 alleles were identified in indica rice.In 295 japonica accessions from northeast Asia,except for the weak functional allele SD1-EQ,sd1-r was the major allele,reducing plant height in comparison with SD1-EQ.Japonica germplasm resources carrying reported sd1 alleles were identified by genotype searching and further verified by literature search,genealogical analysis,and d Caps markers.Pedigrees and geographic distribution showed that sd1-r is an excellent allele widely used in northern China and Tohoku in Japan,and sd1-j is commonly used in east China and Kyushu in Japan.Dongnong-and Xiushui-series cultivars carrying sd1-r and sd1-j,respectively,are essential branches of the backbone parents of Chinese japonica rice,Akihikari and Ce21,with the largest number of descendants and derived generations.In semi-dwarf japonica rice breeding,sd1-d was introgressed into Daohuaxiang 2(DHX2).Dwarf and semi-dwarf lines carrying sd1-d were selected and designated as 1279 and 1280,respectively,after withstanding typhoon-induced strong winds and heavy rains in 2020,and are anticipated to become useful intermediate materials for future genetic research and breeding.This work will facilitate the introduction,parental selection,and marker-assisted breeding,and provide a material basis for the next step in identifying favorable genes that selected together with the sd1 alleles in japonica backbone parents.