A graph-based genome and pan-genome variation of the model plant Setaria.

Setaria italica (foxtail millet), a founder crop of East Asian agriculture, is a model plant for C4 photosynthesis and developing approaches to adaptive breeding across multiple climates. Here we established the Setaria pan-genome by assembling 110 representative genomes from a worldwide collection. The pan-genome is composed of 73,528 gene families, of which 23.8%, 42.9%, 29.4% and 3.9% are core, soft core, dispensable and private genes, respectively; 202,884 nonredundant structural variants were also detected. The characterization of pan-genomic variants suggests their importance during foxtail millet domestication and improvement, as exemplified by the identification of the yield gene SiGW3, where a 366-bp presence/absence promoter variant accompanies gene expression variation. We developed a graph-based genome and performed large-scale genetic studies for 68 traits across 13 environments, identifying potential genes for millet improvement at different geographic sites. These can be used in marker-assisted breeding, genomic selection and genome editing to accelerate crop improvement under different climatic conditions.

Genetic characterization of hull color using BSR-Seq and genome re-sequencing approaches in foxtail millet.

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.

Identification of QTL for resistance to leaf blast in foxtail millet by genome re-sequencing analysis.

KEY MESSAGE: Three QTL for resistance to leaf blast were identified on chromosomes 1, 2, and 8 of the foxtail millet cultivar Yugu 5. Leaf blast disease of foxtail millet (Setaria italica) is caused by Pyricularia spp., can infect all the aboveground parts of plants, and is the most frequently observed blast disease in China. Lack of information on genetic control of disease resistance impedes developing leaf blast-resistant cultivars. An F6 recombinant inbred line (RIL) population from the cross Yugu 5 × Jigu 31 was phenotyped for its reactions to leaf blast in six field trials in the naturally diseased nurseries. An ultra-density genetic linkage map was constructed using 35,065 single nucleotide polymorphism (SNP) markers generated by sequencing of the RIL population. Three QTL, QLB-czas1, QLB-czas2, and QLB-cazas8, were detected in the genomic intervals of 276.6 kb, 1.62 Mb, and 1.75 Mb on chromosomes 1, 2, and 8 of Yugu 5, which explained 14-17% (2 environments), 9% (5 environments), and 12-20% (6 environments) of the phenotypic variations. Bulked segregant analysis (BSA) and RNA sequencing (BSR-Seq) method identified common SNPs that fell in the genomic region of QLB-czas8, providing additional evidence of localization of this QTL. Three and 19 predicted genes were annotated to be associated with disease resistance in the genomic intervals for QLB-czas2 and QLB-czas8. Due to their unique positions, these QTL appear to be new loci conferring resistance to leaf blast. The identification of these new resistance QTL will be useful in cultivar development and the study of the genetic control of blast resistance in foxtail millet.

Variation of B chromosome associated with tissue culture in wheat-rye cross.

In vitro variation of B chromosomes was studied by examining the callus cells derived from the immature embryos from a cross of Chinese Spring wheat (Triticum aestivum L.) and Fin 7416 rye (Secale cereale L.) carrying two B chromosomes. In 40-d-old callus cells, the numbers of B chromosomes ranged from one to four in 65.6% of the cells observed. The distribution of B chromosome numbers was associated with the ploidy levels of the normal chromosomes (A chromosomes). The frequency of the cells with high numbers of B chromosomes (i.e., three or four B chromosomes) in the amphiploid cells with 56 A chromosomes was greater than those in the haploid cells with 28 A chromosomes. Although structural changes in the rye A chromosomes were observed, cytological observation and genomic in situ hybridization demonstrated that the rye B chromosomes were conserved in morphological appearance following tissue culture.