Peanut pod shape is a heritable trait which affects the market acceptance of in-shell peanut products.  In order to determine the genetic control of pod shape, six component traits of pod shape (pod length, pod width, pod length/width ratio, pod roundness, beak degree and constriction degree) were measured using an image-based phenotyping method.  A recombinant inbred line (RIL) population consisting of 181 lines was phenotyped across three environments.  Continuous distributions and transgressive segregations were demonstrated in all measured traits and environments.   Significant correlations were found among most component traits with broad-sense heritability ranging from 0.87 to 0.95.  Quantitative trait locus (QTL) analysis yielded 26 additive QTLs explaining 3.79 to 52.37% phenotypic variations.  A novel, stable and major QTL region conditioning multiple shape features was detected on chromosome 2, which spans a 10.81-Mb genomic region with 543 putative genes.  Bioinformatics analysis revealed several candidate genes in this region.  In addition, 73 pairs of epistatic interactions involving 92 loci were identified for six component traits explaining 0.94–6.45% phenotypic variations.  These results provide new genetic loci to facilitate genomics-assisted breeding of peanut pod shape.

In higher plants, the shoot apical meristem produces lateral organs in a regular spacing (phyllotaxy) and timing (plastochron).  The molecular analysis of mutants associated with phyllotaxy and plastochron would increase our understanding of the mechanism of shoot architecture formation.  In this study, we identified mutant mnd8^ynp5 that shows an increased rate of leaf emergence and a larger number of nodes in combination with a dwarfed growth habit from an EMS-treated population of the elite barley cultivar Yangnongpi 5.  Using a map-based cloning strategy, the mnd8 gene was narrowed down to a 6.7-kb genomic interval on the long arm of chromosome 5H.  Sequence analysis revealed that a C to T single-nucleotide mutation occurred at the first exon (position 953) of HORVU5Hr1G118820, leading to an alanine (Ala) to valine (Val) substitution at the 318th amino acid site.  Next, HORVU5Hr1G118820 was defined as the candidate gene of MND8 encoding 514 amino acids and containing two multidrug and toxic compound extrusion (MATE) domains.  It is highly homologous to maize Bige1 and has a conserved function in the regulation of plant development by controlling the leaf initiation rate.  Examination of modern barely varieties showed that Hap-1 was the dominant haplotype and was selected in barley breeding around the world.  Collectively, our results indicated that mnd8^ynp5 is a novel allele of the HORVU5Hr1G118820 gene that is possibly responsible for the shortened plastochron and many noded dwarf phenotype in barley.

Plant height (PH), primary lateral branch length (PBL) and branch number (BN) are architectural components impacting peanut pod yield, biomass production and adaptivity to mechanical harvesting.  In this study, a recombinant inbred population consisting of 181 individual lines was used to determine genetic controls of PH, PBL and BN across three environments.  Phenotypic data collected from the population demonstrated continuous distributions and transgressive segregation patterns.  Broad-sense heritability of PH, PBL and BN was found to be 0.87, 0.88 and 0.92, respectively.  Unconditional individual environmental analysis revealed 35 additive QTLs with phenotypic variation explained (PVE) ranging from 4.57 to 21.68%.  A two-round meta-analysis resulted in 24 consensus and 17 unique QTLs.  Five unique QTLs exhibited pleiotropic effects and their genetic bases (pleiotropy or tight linkage) were evaluated.  Joint analysis was performed to estimate the QTL by environment interaction (QEI) effects on PH, PBL and BN, which collectively explained phenotypic variations of 10.80, 11.02, and 7.89%, respectively.  We identified 3 major and stable QTL regions (uq9-3, uq10-2 and uq16-1) on chromosomes 9, 10 and 16, spanning 1.43-1.53 Mb genomic regions.  Candidate genes involved in phytohormones biosynthesis, signaling and cell wall development were proposed to regulate these morphological traits.  These results provide valuable information for further genetic studies and development of molecular markers applicable for peanut architecture improvement.