Lodging results in serious yield and quality reductions in foxtail millet (Setaria italica). Among summer crops, foxtail millet is a high density and soft stalked crop that is prone to lodging. Field selection for lodging resistance is difficult because the occurrence of lodging depends on the environmental conditions. A practical method for the evaluation of lodging is not available for foxtail millet, so an understanding of lodging-associated traits and identifying a suitable method to assess lodging are essential to select for lodging resistance and to predict the risk of lodging in a cultivar. In the present study, six stem and root traits associated with lodging was measured in the field and lodging coefficients were determined to evaluate lodging resistance in landrace and improved cultivars. Based on the results of correlation analysis, lodging coefficient is a suitable indicator for field selection for lodging resistance in both classes of cultivars tested for breeding purpose. Statistical analyses demonstrated that lodging was associated with stem quality rather than plant height and internode length at the stem base. The most important trait that directly impacted on lodging coefficient was mechanical strength of the stem and plant height in the landraces, while the weights of the above-and underground tissues, in combination with mechanical strength of the stem, were the most important contributors to lodging coefficient in the improved cultivars.

Lodging can be an important factor in limiting yield and quality of summer foxtail millet [Setaria italica (L.) P. Beauv.]. Although lodging resistance varies among different genotypes, direct selection for lodging resistance is difficult because of its sporadic occurrence in the field and inconsistency between years. A 2-year-field study was conducted with 35 summer foxtail millet cultivars or advanced breeding lines to determine the association between lodging resistance and culm morphology, anatomy and chemical composition. Path analyses indicated that stem-breaking strength had the most important effect on the lodging coefficient. The breaking strength of stem was associated with specific morphological properties of the culm, such as greater culm diameter and most importantly culm wall thickness. Width of sclerenchyma tissue, and the number and sheath width of the large vascular bundles were the major anatomical properties that influenced stem-breaking strength. The cellulose and lignin compositions of the culm had different effects on stem-breaking strength. Cultivars with smaller lodging coefficients contained higher levels of cellulose, but lower levels of lignin than the cultivars that were more prone to lodging. The findings from the present study provide useful information on lodging-associated traits in the culm that can be used as indicators for the improvement of lodging resistance in foxtail millet.

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Hull color of foxtail millet is an important indicator of certain nutritional quality parameters. An F2:6 recombinant inbred line (RIL) population developed by crossing a yellow-hulled cultivar Yugu 5 and a brown-hulled cultivar Jigu 31 was used to determine the genetic control of the hull color trait. This population segregated for yellow and brown hull colors in a ratio of 2:1, indicating that hull color is regulated by multiple genetic loci. A bulk segregant analysis-RNA sequencing (BSR-Seq) approach performed using the RNA bulks from 30 lines with brown and yellow hull colors each identified three genomic regions on chromosomes 1 (4,570,517-10,698,955 bp), 2 (40,301,380-46,168,003 bp), and 3 (44,469,860-50,532,757 bp). A new QTL for brown hull color of Jigu 31, QHC.czas1, was detected between bin markers Block43 and Block697 on chromosome 1 with the genetic linkage map constructed by re-sequencing a subset of the 147 RILs. This QTL explained a high level of phenotypic variation ranging from 28.0% to 47.0%. The corresponding genomic region of this QTL in the foxtail millet reference genome overlapped with that detected on chromosome 1 by the BSR-Seq analysis. Nineteen genes associated with biosynthesis of anthocyanin were annotated in this genomic region. Gene Si1g06530 encoding a SANT/Myb domain protein was highly expressed in developing panicles and seeds, which warrants further verification as the candidate gene for the brown color hull of Jigu 31. Moreover, several annotated genes for biosynthesis of anthocyanin were identified in the genomic regions of chromosomes 2 and 3.