Cong Zhang’s research while affiliated with Sichuan Academy of Environmental Sciences and other places

Sweetpotato (Ipomoea batatas L.), an important food and industrial crop in the world, has a highly heterozygous hexaploid genome, making the development of single nucleotide polymorphism (SNP) markers challenging. Identifying SNP loci and developing practical SNP markers are crucial for genomic and genetic research on sweetpotato. A restriction site-associated DNA sequencing analysis of 60 sweetpotato accessions in this study yielded about 7.97 million SNPs. Notably, 954 candidate SNPs were obtained from 21,681 high-quality SNPs. Based on their stability and polymorphism, 274 kompetitive allele specific PCR (KASP) markers were then developed and uniformly distributed on chromosomes. The 274 KASP markers were used to genotype 93 sweetpotato accessions to evaluate their utility for assessing germplasm and analyzing genetic diversity and population structures. These markers had respective mean values of 0.24, 0.34, 0.31, and 0.25 for minor allele frequency, heterozygosity, gene diversity, and polymorphic information content (PIC). Their genetic pedigree led to the division of all accessions into three primary clusters, which were found to be both interrelated and independent. Finally, 74 KASP markers with PIC values greater than 0.35 were selected as core markers. These markers were used to construct the DNA fingerprints of 93 sweetpotato accessions and were able to differentiate between all accessions. To the best of our knowledge, this is the first attempt at the development and application of KASP markers in sweetpotato. However, due to sweetpotato’s polyploidy, heterozygosity and the complex genome, the KASP marker conversion rate in this study was relatively low. To improve the KASP marker conversion rate, and accuracies in SNP discovery and marker validation, further studies including more accessions from underrepresented regions are needed in sweetpotato.

Sweet potato (Ipomoea batatas (L.) is regarded among the most crucial crops globally because it is abundant in essential nutrients vital for human health. However, limited comprehensive information is available regarding the nutritional composition of sweet potato, which hinders its optimal utilization. This study investigated the nutritional and chemical composition of sweet potato roots and explored their interrelationships. In total, 86 sweet potato accessions, comprising white, yellow, orange, and purple flesh-colored varieties, were used. A total of 34 components, including nutrients, phytochemicals, and minerals, were identified. Multivariate analysis was performed to assess the relationships among these components. The sweet potato roots were rich in carbohydrates, polyphenols, and minerals. Carbohydrates were primarily composed of total starch (22.6–69.7 g/100 g DW), total soluble sugar (TSS) (10.3–40.0 g/100 g DW), and total dietary fiber (TDF) (7.99–26.0 g/100 g DW). Polyphenols included total caffeoylquinic acids (CQAs) (0.478–14.2 g/kg DW), total anthocyanins (0–2003 mg/kg DW), and β-carotene (0–133 mg/kg DW). The mineral content followed the order: potassium > calcium > phosphorus > sodium > magnesium > iron > manganese > zinc > copper > selenium. White-fleshed sweet potato exhibited high total starch levels (50.4 g/100 g DW) but low TSS levels (21.1 g/100 g DW). Orange-fleshed sweet potato contained high levels of TSS (26.5 g/100 g DW), TDF (17.9 g/100 g DW), and β-carotene (61.4 mg/100 g DW) but low levels of protein (2.99 g/100 g DW) and total starch (43.0 g/100 g DW). Purple-fleshed sweet potato had high levels of phytochemicals, particularly total CQAs (8.17 g/kg DW) and anthocyanins (904 mg/kg DW). Cluster analysis categorized sweet potato accessions into six clusters with unique characteristics. Furthermore, principal component analysis identified accessions with exceptionally high nutritional content. The correlation analysis indicated that starch was negatively correlated with soluble sugar and TDF, whereas CQAs and anthocyanins were highly positively correlated. These findings offer a solid theoretical foundation for sweet potato breeding and utilization.

Background: Sweet potato (Ipomoea batatas (L.) Lam.), a key global root crop, faces challenges due to its narrow genetic background. This issue can be addressed by utilizing the diverse genetic resources of sweet potato’s wild relatives, which are invaluable for its genetic improvement. Methods: The morphological differences in leaves, stems, and roots among 13 Ipomoea species were observed and compared. Chromosome numbers were determined by examining metaphase cells from root tips. Fluorescence in situ hybridization (FISH) was used to identify the number of 5S and 18S rDNA sites in these species. PCR amplification was performed for both 5S and 18S rDNA, and phylogenetic relationships among the species were analyzed based on the sequences of 18S rDNA. Results: Three species were found to have enlarged roots among the 13 Ipomoea species. Chromosome analysis revealed that I. batatas had 90 chromosomes, Ipomoea pes-tigridis had 28 chromosomes, while the remaining species possessed 30 chromosomes. Detection of rDNA sites in the 13 species showed two distinct 5S rDNA site patterns and six 18S rDNA site patterns in the 12 diploid species. These rDNA sites occurred in pairs, except for the seven 18S rDNA sites observed in Ipomoea digitata. PCR amplification of 5S rDNA identified four distinct patterns, while 18S rDNA showed only a single pattern across the species. Phylogenetic analysis divided the 13 species into two primary clades, with the closest relationships found between I. batatas and Ipomoea trifida, as well as between Ipomoea platensis and I. digitata. Conclusions: These results enhance our understanding of the diversity among Ipomoea species and provide valuable insights for breeders using these species to generate improved varieties.

Leaf color affects the efficiency of photosynthesis, and leaf color mutants are important genetic materials for studying the mechanisms of photosynthesis, chlorophyll biosynthesis, and chloroplast development in rice. In this study, a white-striped leaf mutant, wst1, was obtained from the mutant population of the indica restorer line ‘Chuanhui 907’ (R907) when treated with ⁶⁰Co-γ radiation. Compared to the wild-type, the wst1 mutant showed normal leaf color before tillering and white stripes on the leaf and leaf sheaths after tillering. The chlorophyll and carotenoid contents were significantly reduced, and the thylakoids of chloroplasts developed abnormalities in wst1 plants in the tillering stage. The results of agronomic trait analysis showed that the number of effective panicles, plant height, seed setting rate, and 1000-grain weight of the wst1 mutant were significantly lower than those of the wild-type. Genetic analysis revealed that the phenotype of the wst1 mutant is controlled by a pair of recessive nuclear genes. The candidate gene was mapped to a 72 kb region between the InDel markers M6 and M12 on the short arm of chromosome 1 using molecular marker linkage analysis. Candidate genes were sequenced on the interval, and a G base was replaced by A at the 6972nd position on the 16th exon of LOC_Os01g01920, which encoded a previously reported protein containing the HD domain, WSF3/WFSL1, leading to alternative splicing, causing a 104 bp deletion in the coding region, and resulting in mistranslation after the 490 amino acid of the encoded protein translation in wst1. RT-qPCR analysis showed that the expression levels of most genes related to chlorophyll synthesis and chloroplast development were significantly altered in wst1 plants. Our study identified a novel allele of wsf3 and wfsl1 mutant and provided a new genetic resource and theoretical basis for further understanding of the molecular mechanism of WST1 gene regulation of white-striped leaves in rice.

The medicinal fungus Wolfiporia cocos colonizes and then grows on the wood of Pinus species, and utilizes a variety of Carbohydrate Active Enzymes (CAZymes) to degrades wood for the development of large sclerotia that is mostly built up of beta-glucans. Some differentially expressed CAZymes were revealed by comparisons between the mycelia cultured on potato dextrose agar (PDA) and sclerotia formed on pine logs in previous studies. Here, different profile of expressed CAZymes were revealed by comparisons between the mycelia colonization on pine logs (Myc.) and sclerotia (Scl.b). To further explore the regulation and function of carbon metabolism in the conversion of carbohydrates from Pine species by W. cocos, the transcript profile of core carbon metabolism was firstly analyzed, and it was characterized by the up-regulated expression of genes in the glycolysis pathway (EMP) and pentose phosphate pathway (PPP) in Scl.b, as well as high expression of genes in the tricarboxylic acid cycle (TCA) in both Myc. and Scl.b stages. The conversion between glucose and glycogen and between glucose and β-glucan was firstly identified as the main carbon flow in the differentiation process of W. cocos sclerotia, with a gradual increase in the content of β-glucan, trehalose and polysaccharide during this process. Additionally, gene functional analysis revealed that the two key genes (PGM and UGP1) may mediate the formation and development of W. cocos sclerotia possibly by regulating β-glucan synthesis and hyphal branching. This study has shed light on the regulation and function of carbon metabolism during large W. cocos sclerotium formation and may facilitate its commercial production.

Leaf color affects the efficiency of photosynthesis, and leaf color mutants are important genetic materials for studying the mechanisms of photosynthesis, chlorophyll biosynthesis, and chloroplast development in rice. In this study, a white-striped leaf mutant, wst1 , was obtained from the mutant population of the indica restorer line ‘Chuanhui 907’ (R907) when treated by ⁶⁰ Co-γ radiation. Compared to the wild-type, the wst1 mutant showed normal leaf color before tillering and white stripes on the leaf and leaf sheaths after tillering. The chlorophyll and carotenoid contents were significantly reduced, and the thylakoids of chloroplasts developed abnormalities in wst1 plants in the tillering stage. The results of agronomic trait analysis showed that the number of effective panicles, plant height, seed setting rate, and 1000-grain weight of the wst1 mutant were significantly lower than those of the wild-type. Genetic analysis revealed that the phenotype of the wst1 mutant is controlled by a pair of recessive nuclear genes. The candidate gene was mapped to a 72 kb region between the InDel markers M6 and M12 on the short arm of chromosome 1 using molecular marker linkage analysis. Candidate genes were sequenced on the interval, and a G base was replaced by A at the 6972nd position on the 16th exon of LOC_Os01g01920 , which encoded a previously reported protein containing the HD domain, WSF3/WFSL1, leading to alternative splicing, causing a 104 bp deletion in the coding region, and resulting in mistranslation after the 490 amino acid of the encoded protein translation in wst1. RT-qPCR analysis showed that the expression levels of most genes related to chlorophyll synthesis and chloroplast development were significantly altered in wst1 plants. Our study identified a novel allele of wsf3 and wfsl1 mutant and provided a new genetic resource and theoretical basis for further understanding of the molecular mechanism of WST1 gene regulation of white-striped leaves in rice.

Expansins play important roles in root growth and development, but investigation of the expansin gene family has not yet been reported in Ipomoea trifida, and little is known regarding storage root (SR) development. In this work, we identified a total of 37 expansins (ItrEXPs) in our previously reported SR-forming I. trifida cv. Y22 genome, which included 23 ItrEXPAs, 4 ItrEXPBs, 2 ItrEXLAs and 8 ItrEXLBs. The phylogenetic relationship, genome localization, subcellular localization, gene and protein structure, promoter cis-regulating elements, and protein interaction network were systematically analyzed to reveal the possible roles of ItrEXPs in the SR development of I. trifida. The gene expression profiling in Y22 SR development revealed that ItrEXPAs and ItrEXLBs were down-regulated, and ItrEXPBs were up-regulated while ItrEXLAs were not obviously changed during the critical period of SR expansion, and might be beneficial to SR development. Combining the tissue-specific expression in young SR transverse sections of Y22 and sweetpotato tissue, we deduced that ItrEXLB05, ItrEXLB07 and ItrEXLB08 might be the key genes for initial SR formation and enlargement, and ItrEXLA02 might be the key gene for root growth and development. This work provides new insights into the functions of the expansin gene family members in I. trifida, especially for EXLA and EXLB subfamilies genes in SR development.

As one of the important traits, hull color is the morphological marker of rice, which plays an important role in the mechanized color selection of hybrid rice seed production but lacks good application. Here, we obtained a reddish-brown hull 1 (rbh1) mutant from an Indica maintainer material H9808 by aerospace mutagenesi. In the rbh1 mutant, the hull color was reddish brown, and the grain width and 1000-grain weight decreased significantly, but the other agronomic traits did not change significantly. Furthermore, the total flavonoids and anthocyanin content in the rbh1 hulls deposition was remarkably higher than WT, and the lignin level in the rbh1 hull was reduced. Genetic analysis indicated that the reddish-brown hull trait was controlled by a pair of recessive nuclear genes. Map-based cloning indicated that RBH1 was located within the physical distance of 48 kb on the short arm of chromosome 2. The comparative analysis of genome DNA sequence between rbh1 and WT found that a substitution from T to C (+ 1001) occurred in the fourth exon of LOC_Os02g09490 in rbh1 mutant. Genetic complementation experiments indicate that RBH1 is an allele of the previously reported GH2, which encoding a cinnamyl alcohol dehydrogenase protein involving in lignin biosynthesis. qRT-PCR showed that the relative expression of lignin and flavonoid-related genes in the hulls of rbh1 mutant was significantly upregulated, confirming that GH2/RBH1 is an important gene in the metabolism of lignin and flavonoids; and provides material basis for further studying the mechanism of GH2/RBH1 regulating the rice hull color.. In addition, the hybrid F1 combination analysis indicated that the rbh1 mutation site did not affect the agronomic traits and yield of the hybrid rice, which was to cultivate the rbh1 locus into a new sterile line or restorer line with reddish-brown hulls and rice breeding application of rbh1 locus on mechanized seed production of hybrid rice provides a theoretical basis.

Sweetpotato (Ipomoea batatas L.) is one of the most important food and grain-forage crops globally. It has been planted in >100 countries. Due to the complexity of the sweetpotato genome, its research is far behind other major food crops. At present, limited information about the sweetpotato genome is available. Thus, it is central to find an efficient approach for the investigation of sweetpotato genome. In this study, RAD-seq (Restriction site-associated DNA sequencing) was used to evaluate sweetpotato genetic structure diversity and to develop relevant SSR markers. The study yielded >128 Gb reliable sequence data from 81 sweetpotato accessions. By analyzing polymorphic tags from each accession, a total of 55,622 restriction-site associated DNA sequencing tags (RAD-seq) were found, containing 907,010 SNP. Genetic analysis divided 81 accessions into five major clusters based on their SNP genotype, which matches the results of genetic analysis and the genetic family tree. In addition, 18,320 SSRs loci were detected and 9336 SSR primer pairs were developed. Eighty-three primer pairs were amplified in different sweetpotato genotypes, 76 of which successfully amplified polymorphism bands. These results provide significant information about sweetpotato genome, which can be used to identify novel gene and to further develop the gene chip. And more significant, clustering results based on the SNP genotype provide an essential reference for breeders to match parent plants in breeding program. Additionally, SSR markers developed in this study will supply a wealth of markers for marker-assisted selection in sweetpotato breeding.