Genetic diversity and population structure of Plenodomus biglobosus on flixweed (Descurainia sophia) in northwestern China.

Plenodomus biglobosus (Pb), a causal agent of blackleg of rapeseed, is composed of several subspecies, including 'australensis' (Pba), 'brassicae' (Pbb) and 'canadensis' (Pbc). Besides rapeseed, Pb can infect many wild cruciferous plants (WCPs), such as flixweed (Descurainia sophia) and pennycress (Thlaspi arvense), which may become the infection source for blackleg of rapeseed. However, Pb on WCPs has not been well investigated in China. This study identified the blackleg fungi on two WCPs in Sayram Lake and Zhaosu County in Xinjiang of China: flixweed (15 isolates) and pennycress (1 isolate) as well as on rapeseed (971 isolates). They belonged to Pba (11), Pbb (18) and Pbc (958). Pba occurred on flixweed (10) and pennycress (1) only in Sayram Lake, whereas Pbb and Pbc occurred on flixweed (1 and 4 isolates, respectively) and rapeseed (17 and 954 isolates, respectively) in Zhaosu County. Then, virulence of 16 isolates from flixweed and pennycress was determined on rapeseed. Their genomes were sequenced and used to identify the mating-type idiomorphs and to analyze population genetic structure. Results showed that all of the 16 isolates were virulent to rapeseed. Only MAT1-1 was detected in 11 Pba isolates, implying that Pba may lack sexual reproduction. The 16 isolates from two WCPs were divided into four genetic groups: Group I for Pbc (4 isolates), Group II for Pbb (1 isolate), and Group III (3 isolates) and IV (8 isolates) for Pba. The findings about the single mating-type in Pba and its limited geographic distribution provided a case showing the importance of sexual reproduction in epidemics of Pb. To the best of our knowledge, this is the first report of Pba, Pbb and Pbc on flixweed, and Pba on pennycress in China.

Genome-wide identification and comprehensive analysis of WRKY transcription factor family in safflower during drought stress.

The WRKY family is an important family of transcription factors in plant development and stress response. Currently, there are few reports on the WRKY gene family in safflower (Carthamus tinctorius L.). In this study, a total of 82 CtWRKY genes were identified from the safflower genome and could be classified into 3 major groups and 5 subgroups based on their structural and phylogenetic characteristics. The results of gene structure, conserved domain and motif analyses indicated that CtWRKYs within the same subfamily maintained a consistent exon/intron organization and composition. Chromosomal localization and gene duplication analysis results showed that CtWRKYs were randomly localized on 12 chromosomes and that fragment duplication and purification selection may have played an important role in the evolution of the WRKY gene family in safflower. Promoter cis-acting element analysis revealed that the CtWRKYs contain many abiotic stress response elements and hormone response elements. Transcriptome data and qRT-PCR analyses revealed that the expression of CtWRKYs showed tissue specificity and a strong response to drought stress. Notably, the expression level of the CtWRKY55 gene rapidly increased more than eightfold under drought treatment and rehydration, indicating that it may be a key gene in response to drought stress. These results provide useful insights for investigating the regulatory function of the CtWRKY gene in safflower growth and development, as well as identifying key genes for future molecular breeding programmes.

Whole-genome and genome-wide association studies improve key agricultural traits of safflower for industrial and medicinal use.

Safflower (Carthamus tinctorius) is widely cultivated around the world for its seeds and flowers. The presence of linoleic acid (LA) in its seeds and hydroxysafflor yellow A (HSYA) in its flowers are the crucial traits that enable safflower to be used for industrial and medicinal purposes. Understanding the genetic control of these traits is essential for optimizing the quality of safflower and its breeding. To further this research, we present a chromosome-scale assembly of the genome of the safflower variety 'Chuanhonghua 1', which was achieved using an integrated strategy combining Illumina, Oxford Nanopore, and Hi-C sequencing. We obtained a 1.17-Gb assembly with a contig N50 of 1.08 Mb, and all assembled sequences were assigned to 12 pseudochromosomes. Safflower's evolution involved the core eudicot γ-triplication event and a whole-genome duplication event, which led to large-scale genomic rearrangements. Extensive genomic shuffling has occurred since the divergence of the ancestor of dicotyledons. We conducted metabolite and transcriptome profiles with time- and part-dependent changes and screened candidate genes that significantly contribute to seed lipid biosynthesis. We also analyzed key gene families that participate in LA and HSYA biosynthesis. Additionally, we re-sequenced 220 safflower lines and carried out a genome-wide association study using high-quality SNP data for eight agronomic traits. We identified SNPs related to important traits in safflower. Besides, the candidate gene HH_034464 (CtCGT1) was shown to be involved in the biosynthesis of HSYA. Overall, we provide a high-quality reference genome and elucidate the genetic basis of LA and HSYA biosynthesis in safflower. This vast amount of data will benefit further research for functional gene mining and breeding in safflower.

Genomic insights into the origin, domestication and diversification of Brassica juncea.

Despite early domestication around 3000 BC, the evolutionary history of the ancient allotetraploid species Brassica juncea (L.) Czern & Coss remains uncertain. Here, we report a chromosome-scale de novo assembly of a yellow-seeded B. juncea genome by integrating long-read and short-read sequencing, optical mapping and Hi-C technologies. Nuclear and organelle phylogenies of 480 accessions worldwide supported that B. juncea is most likely a single origin in West Asia, 8,000-14,000 years ago, via natural interspecific hybridization. Subsequently, new crop types evolved through spontaneous gene mutations and introgressions along three independent routes of eastward expansion. Selective sweeps, genome-wide trait associations and tissue-specific RNA-sequencing analysis shed light on the domestication history of flowering time and seed weight, and on human selection for morphological diversification in this versatile species. Our data provide a comprehensive insight into the origin and domestication and a foundation for genomics-based breeding of B. juncea.