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Hollyhock (Alcea rosea (Linn). Cavan) is an herbaceous flowering plant with significant applications in urban greening, soil remediation, and traditional medicine. However, its genetic diversity and molecular characteristics at the population level have not been explored yet. Here, the phenotypic and genetic diversity of 162 hollyhock accessions from China revealed extensive variation among 11 traits and strong correlations between several quantitative traits. Whole-genome re-sequencing of 32 randomly chosen accessions identified 10,468,760 core single-nucleotide polymorphisms (SNPs) distributed evenly across the genome, except for on chromosome 21, and the average nucleotide diversity (π) was calculated to be 0.00397. Principal component analysis showed that these 32 accessions could be divided into four subpopulations, which was in agreement with the population structure analysis, and the subpopulations were strongly correlated with geographic location. A neighbor-joining dendrogram displayed similar clusters, except for accessions HuB25 and HLJ28, which formed two separate clusters. Our findings illuminate the genetic diversity in hollyhock and provide valuable information for hollyhock breeding. [ABSTRACT FROM AUTHOR]

Chinese cabbage (Brassica rapa L.) is one of the most important and highly nutritious vegetables in China belonging to the Brassicaceae family. Flowering or bolting is one of the most critical developmental stages in flowering plants. For the spring-sown Chinese cabbage, late-bolting is desirable over early-bolting according to consumer preferences. We determined the inheritance pattern of the late-bolting trait using F1 and F2 generated from a cross between 'SY2004' (late-bolting) and 'CX14-1' (early-bolting). The genetic analysis revealed that the late-bolting to early-bolting trait was controlled by an incomplete dominant gene that we named BrLb-1. Furthermore, we performed bulked segregant analysis (BSA) via whole genome re-sequencing and the results showed that this gene was harbored on the chromosome A07 at the intersections of 20,070,000 to 25,290,000 bp and 20,330,000 to 25,220,000, an interval distance of 4.89 Mb. In this candidate interval, totals of 2321 and 1526 SNPs with non-synonymous mutations, and 229 and 131 InDels with frameshift mutations, were found between the parents and the bulked pools, respectively. Furthermore, we identified three putative candidate genes for the late-bolting trait, including BraA07g029500, BraA07g029530 and BraA07g030360, which code for the AGAMOUS-like MADS-box protein AGL12, a pentatricopeptide repeat-containing protein and NAC transcription factor 29, respectively; however, further functional analysis is required. These genetic variants could be utilized for the further development of molecular markers for marker-assisted breeding in Chinese cabbage. [ABSTRACT FROM AUTHOR]

Summary: Bohai Black (BHB) cattle, one of eight representative indigenous breeds in China, is well known for its high resistance to disease, endurance under unfavorable feeding conditions and excellent meat quality. Over recent, the number of BHB cattle has decreased sharply. To investigate the population structure and genetic diversity of this breed, the whole‐genome data of 35 individuals from a conservation farm were obtained using the Illumina 150 bp paired‐end platform. The results of the genetic structure and diversity analyses showed that BHB cattle had mixed Bos taurus and Bos indicus ancestry, close phylogenic relationships with Jiaxian Red and Luxi cattle and abundant genetic diversity. The bulls tested here could be divided into six families. This study presents a comprehensive evaluation of the genetic structure and diversity of the BHB cattle, and lays the theoretical basis for conservation and utilization of the valuable germplasm resource. [ABSTRACT FROM AUTHOR]

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• A weak phylogeographic sub-structure was observed within Colletotrichum acutatum species complex from rubber trees in China. • Genetic recombination is main patterns of genetic variation within Colletotrichum acutatum species complex from rubber trees in China. • Morphological characters and levels of aggressiveness between populations show significant differences. The Colletotrichum acutatum species complex possesses a diverse number of important traits, such as a wide host range and host preference, different modes of reproduction, and different strategies of host infection. Research using comparative genomics has attempted to find correlations between these traits. Here, we used multi-locus techniques and gene genealogical concordance analysis to investigate the phylogenetic relationships and taxonomic status of the Colletotrichum acutatum species complex using field isolates obtained from rubber trees. The results revealed that the dominant species was C. australisinense , followed by C. bannaense , while strain YNJH17109 was identified as C. laticiphilum. The taxonomic status of strains YNLC510 and YNLC511 was undetermined. Using whole-genome single nucleotide polymorphism data to analyze population structure, 18 strains of C. australisinense were subsequently divided into four populations, one of which was derived from an admixture of two populations. In addition, the strains LD1687, GD1628, and YNLC516, did not belong to any populations, and were considered to be admixtures of two or more populations. A split decomposition network analysis also provided evidence for genetic recombination within Colletotrichum acutatum species complex from rubber trees in China. Overall, a weak phylogeographic sub-structure was observed. Analysis also revealed significant differences in morphological characters and levels of virulence between populations. [ABSTRACT FROM AUTHOR]

Identifying alleles associated with adaptation to new environments will advance our understanding of evolution from the molecular level. Previous studies have found that the Populus davidiana southwest population in East Asia has differentiated from other populations in the range. We aimed to evaluate the contributions of the ancestral-state bases (ASBs) relative to derived bases (DBs) in the local adaptation of P. davidiana in the Yunnan-Guizhou Plateau from a quantitative perspective using whole-genome re-sequencing data from 90 P. davidiana samples from three regions across the species range. Our results showed that the uplift of the Qinghai-Tibet Plateau during the Neogene and associated climate fluctuations during the Middle Pleistocene were likely an important factor in the early divergence of P. davidiana . Highly differentiated genomic regions between populations were inferred to have undergone strong linked natural selection, and ASBs are the chief means by which populations of P. davidiana adapt to novel environmental conditions; however, when adapting to regions with high environmental differences relative to the ancestral range, the proportion of DBs was significantly higher than that of background regions, as ASBs are insufficient to cope with these environments. Finally, a number of genes were identified in the outlier region.

Sex dimorphism of economic traits such as growth rate and body size have potential breeding value in aquaculture. Largemouth bass (Micropterus salmoides L.) is an important freshwater cultured fish in China and the females live longer and reach larger sizes than males. However, the lacking of sex-specific makers and the unclear sex determination mechanism inhibits the development of all-female breeding. In this study, 5 females and 5 males were randomly selected and sequenced with whole-genome re-sequencing technology. In total, 1394 filtered SNPs and 425 filtered InDels were finally identified, and most of these makers were located at Chr7 and Chr18. The validation of the 35 SNPs located at Chr7 in three distinct population (n = 72) indicated that 2 SNPs (S4 and S6) could distinguish the females and males with 100% accuracies, which were genotyped as CC and CG, AA and AT in the females and males, respectively. Further, 10 and 6 InDels with sizes more than 18 bp were finally screened out on Chr7 and Chr18. 2 male-specific InDels (rs3394676 and rs3496814) located at Chr7 could effectively distinguish the above females and males with a PCR-based agarose gel electrophoresis, which performed as one band in the females and two bands in the males, respectively. These results suggested the Chr7 might be the sex chromosome and a XX/XY sex determination system in largemouth bass. In conclusion, a whole-genome re-sequencing method was first conducted to provide usefulness sex-specific makers and a XX/XY sex determination system in largemouth bass, which contributes to study of the sex determination mechanisms and the development of mono-sex population breeding. • Whole-genome re-sequencing were first conducted to explore the genetic differences between males and females in largemouth bass. • Two male-specific SNPs and two male-specific InDels were developed to distinguish genetic sex of largemouth bass. • The chromosome 7 was the sex chromosome in largemouth bass. • The sex determination system was a XX/XY determination system in largemouth bass. [ABSTRACT FROM AUTHOR]