First report of root rot caused by Fusarium nygamai on foxtail millet (Setaria italica) in China.

Foxtail millet [Setaria italica (L.) P. Beauv.] is one of the most important nutritious food crops in China. In August 2020, plants of the foxtail millet cultivar Xiao Huang Miao were found that were wilted and root rot symptoms of 25-75% incidence in a field production area of about 3000 m2 near Tongliao of Inner Mongolia and Chaoyang cities of Liaonning province. The wilted plants showed yellowing, stunting, and the lower stalk became straw colored, softened, with gray-white mould on the surface of the stem nodes. The root system was poorly developed, brown and rotted. Symptomatic roots were surface-disinfested with 70% ethanol for 1 min and in 2% sodium hypochlorite (NaOCl) for 3 min, rinsed with sterilized water three times, and placed on potato dextrose agar (PDA) and incubated at 26ºC for 5 days. Ten pure cultures were obtained from single conidia with an inoculation needle under stereomicroscope. The cultures were transferred to carnation leaf agar (CLA) medium and incubated two weeks in the dark at 26ºC for microscopic observation. Macroconidia had one to four septa (three septa dominated), and were slender and straight with curved apical cell and foot-shaped basal cell, 25.5 - 30.5 × 2.5 - 4.5 µm (n=50). Microconidia were non-septate, oval, and were formed in short chains or false heads on monophialides, 2.5 - 15 × 2.75 - 4.0 µm (n=50). Chlamydospores were singly or in chains, circular or subcircular, 5.25 - 11.5 µm in diameter (n=50). Morphologically, the fungus was identified as Fusarium nygamai Burgess & Trimboli (Klaasen and Nelson,1998; Leslie and Summerell, 2006,). To validate this identification, rDNA internal transcribed spacer (ITS), partial translation elongation factor 1 alpha (TEF-á) gene, and RNA polymerase II second largest subunit (rpb2) of the ten isolates were amplified and sequenced (White et al.1990;O'Donnell K. et al. 2015,2010). Identical sequences were obtained and the sequence of the isolate GZGF23 was submitted to GenBank. BLASTn analysis of the ITS (OL964384), TEF-á (OL961517) and RPB2(ON756204) sequence of isolate GZGF23 revealed 99.86% (MH862671, 557/565bp), 100% (MT011009, 713/1770bp) and 100% (MT010976, 1002/3907bp) sequence similarity respectively with F. nygamai (CBS749.97). Pathogenicity studies were conducted on outdoor potted ground and with the foxtail millet cultivar "Xiao Huang miao". Five 12-L pots were filled with sterilized field soil mixed with 300ml conidial suspension at 3 × 105 spores/ml. Another five 12-L pots were filled with sterilized field soil mixed with 300ml sterilized water that served as controls. About twenty seeds per pot were surface disinfected in 2% NaOCl for 3 min, and rinsed with sterilized water. The foxtail millet seeds were sown the same day as soil inoculation and 6 plants were left in each pot when seedling emerged. Five weeks after seedling emergence, all inoculated plants exhibited symptoms similar to the syptoms observed in the field but control plants had no symptoms. The same results were obtained when pathogenicity tests were repeated two times in the same manner. Fusarium nygamai was reisolated from inoculated plants and its morphological and molecular characteristics matched the original isolate, but the fungus was not reisolated from control plants. This is the first report of root rot caused by F. nygamai on foxtail millet in China. The disease might bring a threat to foxtail millet production and effective control measures should be identified to reduce losses. References: Klaasen J. A. and Nelson P. E. 1998. Mycopathologia 140: 171-176. Leslie J. F. and Summerell B. A. 2006. Blackwell Publishing, Oxford, U.K. O'Donnell K., et al. 2015. Phytoparasitica 43:583-595. White T. J., et al. 1990. Academic Press, San Diego, CA, pp 315-322. O'Donnell K et al. 2010. J.Clin.Microbiol. 48:3708.

Genetic control and phenotypic characterization of panicle architecture and grain yield-related traits in foxtail millet (Setaria italica).

KEY MESSAGE: Multi-environment QTL mapping identified 23 stable loci and 34 co-located QTL clusters for panicle architecture and grain yield-related traits, which provide a genetic basis for foxtail millet yield improvement. Panicle architecture and grain weight, both of which are influenced by genetic and environmental factors, have significant effects on grain yield potential. Here, we used a recombinant inbred line (RIL) population of 333 lines of foxtail millet, which were grown in 13 trials with varying environmental conditions, to identify quantitative trait loci (QTL) controlling nine agronomic traits related to panicle architecture and grain yield. We found that panicle weight, grain weight per panicle, panicle length, panicle diameter, and panicle exsertion length varied across different geographical locations. QTL mapping revealed 159 QTL for nine traits. Of the 159 QTL, 34 were identified in 2 to 12 environments, suggesting that the genetic control of panicle architecture in foxtail millet is sensitive to photoperiod and/or other environmental factors. Eighty-eight QTL controlling different traits formed 34 co-located QTL clusters, including the triple QTL cluster qPD9.2/qPL9.5/qPEL9.3, which was detected 23 times in 13 environments. Several candidate genes, including Seita.2G388700, Seita.3G136000, Seita.4G185300, Seita.5G241500, Seita.5G243100, Seita.9G281300, and Seita.9G342700, were identified in the genomic intervals of multi-environmental QTL or co-located QTL clusters. Using available phenotypic and genotype data, we conducted haplotype analysis for Seita.2G002300 and Seita.9G064000,which showed high correlations with panicle weight and panicle exsertion length, respectively. These results not only provided a basis for further fine mapping, functional studies and marker-assisted selection of traits related to panicle architecture in foxtail millet, but also provide information for comparative genomics analyses of cereal crops.

QTL mapping for foxtail millet plant height in multi-environment using an ultra-high density bin map.

KEY MESSAGE: Using a fixed RIL population derived from a widely used foxtail millet backbone breeding line and an elite cultivar, we constructed a high-density bin map and identified six novel multi-environment effect QTLs and seven candidate genes for dwarf phenotype. Plant height is an important trait that determines tradeoffs between competition and resource allocation, which is crucial for yield potential. To improve the C4 model plant foxtail millet (Setaria italica) productivity, it is necessary to isolate plant height-related genes that contribute to ideal plant architecture in breeding. In the present study, we generated a foxtail millet population of 333 recombinant inbred lines (RILs) derived from a cross between a backbone line Ai 88 and an elite cultivar Liaogu 1. We evaluated plant height in 13 environmental conditions across 4 years, the mean plant height of the RIL population ranged from 89.5 to 149.9 cm. Using deep re-sequencing data, we constructed a high-density bin map with 3744 marker bins. Quantitative trait locus (QTL) mapping identified 26 QTLs significantly associated with plant height. Of these, 13 QTLs were repeatedly detected under multiple environments, including six novel QTLs that have not been reported before. Seita.1G242300, a gene encodes gibberellin 2-oxidase-8, which was detected in nine environments in a 1.54-Mb interval of qPH1.3, was considered as an important candidate gene. Moreover, other six genes involved in GA biosynthesis or signaling pathways, and fifteen genes encode F-box domain proteins which might function as E3 ligases, were also considered as candidate genes in different QTLs. These QTLs and candidate genes identified in this study will help to elucidate the genetic basis of foxtail millet plant height, and the linked markers will be useful for marker-assistant selection of varieties with ideal plant architecture and high yield potential.

A haplotype map of genomic variations and genome-wide association studies of agronomic traits in foxtail millet (Setaria italica).

Foxtail millet (Setaria italica) is an important grain crop that is grown in arid regions. Here we sequenced 916 diverse foxtail millet varieties, identified 2.58 million SNPs and used 0.8 million common SNPs to construct a haplotype map of the foxtail millet genome. We classified the foxtail millet varieties into two divergent groups that are strongly correlated with early and late flowering times. We phenotyped the 916 varieties under five different environments and identified 512 loci associated with 47 agronomic traits by genome-wide association studies. We performed a de novo assembly of deeply sequenced genomes of a Setaria viridis accession (the wild progenitor of S. italica) and an S. italica variety and identified complex interspecies and intraspecies variants. We also identified 36 selective sweeps that seem to have occurred during modern breeding. This study provides fundamental resources for genetics research and genetic improvement in foxtail millet.