Transcriptome Analysis of Molecular Mechanisms Underlying Phenotypic Variation in Phaseolus vulgaris Mutant‘nts’

The phenotype of a common bean plant is often closely related to its yield,and the yield of plants with reduced height or poor stem development during growth is low.Mutants serve as an essential gene resource for common bean breeding genetic research.Although model plants and crops are studied to comprehend the molecular mechanisms and genetic basis of plant phenotypes,the molecular mechanism of phenotypic variation in common beans remains underexplored.We here used the mutant‘nts’as material for transcriptome sequencing analysis.This mutant was obtained through 60Co-γirradiation from the common bean variety‘A18’.Differentially expressed genes were mainly enriched in GO functional entries such as cell wall organization,auxin response and transcription factor activity.Metabolic pathways significantly enriched in KEGG analysis included plant hormone signal transduction pathways,phenylpropanoid biosynthesis pathways,and fructose and mannose metabolic pathways.AUX1(Phvul.001G241500),the gene responsible for auxin transport,may be the key gene for auxin content inhibition.In the plant hormone signal transduction pathway,AUX1 expression was downregulated and auxin transport across the membrane was blocked,resulting in stunted growth of the mutant‘nts’.The results provide important clues for revealing the molecular mechanism of‘nts’phenotype regulation in bean mutants and offer basic materials for breeding beneficial phenotypes of bean varieties.

HTPdb and HTPtools:Exploiting maize haplotypetag polymorphisms for germplasm resource analyses and genomics-informed breeding

Along with rapid advances in high-throughput-sequencing technology,the development and application of molecular markers has been critical for the progress that has been made in crop breeding and genetic research.Desirable molecular markers should be able to rapidly genotype tens of thousands of breeding accessions with tens to hundreds of markers.In this study,we developed a multiplex molecular marker,the haplotype-tag polymorphism(HTP),that integrates Maize6H-60K array data from 3,587 maize inbred lines with 6,375 blocks from the recombination block map.After applying strict filtering criteria,we obtained 6,163 highly polymorphic HTPs,which were evenly distributed in the genome.Furthermore,we developed a genome-wide HTP analysis toolkit,HTPtools,which we used to establish an HTP database(HTPdb)covering the whole genomes of 3,587 maize inbred lines commonly used in breeding.A total of 172,921 non-redundant HTP allelic variations were obtained.Three major HTPtools modules combine seven algorithms(e.g.,chain Bayes probability and the heterotic-pattern prediction algorithm)and a new plotting engine named“BCplot”that enables rapid visualization of the background information of multiple backcross groups.HTPtools was designed for big-data analyses such as complex pedigree reconstruction and maize heterotic-pattern prediction.The HTP-based analytical strategy and the toolkit developed in this study are applicable for high-throughput genotyping and for genetic mapping,germplasm resource analyses,and genomics-informed breeding in maize.

A single-nucleotide polymorphism in Pv PW1 encodingβ-1,3-glucanase 9 is associated with pod width in Phaseolus vulgaris L.

Pod width influences pod size,shape,yield,and consumer preference in snap beans(Phaseolus vulgaris L.).In this study,we map Pv PW1,a quantitative trait locus associated with pod width in snap beans,through genotyping and phenotyping of recombinant plants.We identify Phvul.006G072800,encoding theβ-1,3-glucanase 9 protein,as the causal gene for Pv PW1.The Pv PW1^(G3555)allele is found to positively regulate pod width,as revealed by an association analysis between pod width phenotype and the Pv PW1^(G3555C)genotype across 17 bi-parental F_(2)populations.In total,97.7%of the 133 wide pod accessions carry Pv PW1^(G3555),while 82.1%of the 78 narrow pod accessions carry Pv PW1C3555,indicating strong selection pressure on Pv PW1 during common bean breeding.Re-sequencing data from 59 common bean cultivars identify an 8-bp deletion in the intron linked to Pv PW1C3555,leading to the development of the In Del marker of Pv M436.Genotyping 317 common bean accessions with Pv M436 demonstrated that accessions with Pv M436^(247)and Pv M436^(227)alleles have wider pods compared to those with Pv M436^(219)allele,establishing Pv M436 as a reliable marker for molecular breeding in snap beans.These findings highlight Pv PW1 as a critical gene regulating pod width and underscore the utility of Pv M436 in marker-assisted selection for snap bean breeding.