Pan-genome analysis sheds light on structural variation-based dissection of agronomic traits in melon crops

Transcriptome profiling of fruits at different development stages in the Field Muskmelon (Cucumis melo L. var. agrestis Naud.) "Mapao 1"

The Field Muskmelons, showing typically feral morphologies, are essential gene pools for the genetic improvement of cultivated melons. However, the potential gene networks of fruit growth and development in the Field Muskmelon are still poorly understood. Hence, a variety of Field Muskmelon "Mapao 1" showing typical features of the Field Muskmelon and having unique sweet and sour tastes was used in this study. The dynamic changes of the fruit weight, size, and shape of "Mapao 1" and the sugar, dry matter, and total acid contents in fruits of "Mapao 1" were checked with fruit samples collected at 7, 14, 21, 28, and 35 DAP. Given the significant differences in fruit size/shape and sucrose and acid contents at 7 and 28 DAP "Mapao1" fruits, transcriptomics was conducted to reveal their transcriptomic reprogramming between the 7 and 28 DAP fruit samples. A total of 3266 DEGs were up-regulated in the 7 DAP fruits, while there were 1329 up-regulated DEGs in the 28 DAP fruits. Furthermore, the DEGs potentially related to the fruit development and the sweetness and sourness were also discussed in the present work. The potential functions of DEG MELO3C005560 (CmINV1) encoding acid invertase, a key enzyme of sugar metabolism, were preliminarily explored from gene expression, phylogenic analysis, and subcellular localization, in which CmINV1 showed the highest expression level in fruits at the 7 DAP and the lowest level at the 14 DAP; CmINVI had the highest identity with that of cucumber (Cucumis sativus XP 004147588.1); the GFP-CmINV1 fusion protein was located on the plasma membrane. Results of this work provided valuable information about the key genes related to not only fruit growth and development, but also the sourness and sweetness formation in the Field Muskmelon.

The chromosome-scale genomes of two cultivated safflowers (Carthamus tinctorius) provide insights into the genetic diversity resulting from domestication

KEY MESSAGE

Two cultivated safflowers from distinct areas elucidate the genetic diversity present in the linoleic acid biosynthesis, flowering time and flavonoid biosynthesis. The process of domestication facilitates the adaptation of crops to agricultural environments. In this study, we selected two representative safflower cultivars that has been domesticated in two distinct areas in China as samples to investigate their genetic diversity due to local environmental adaption. Yunhong-7 is a locally bred safflower (Carthamus tinctorius) cultivar, that has been currently widely cultivated in Yunnan Province, Southwest China, and Anhui-1 is a safflower cultivar that was locally bred in Anhui Province, East China. We firstly generated the chromosome-scale genome assembly for yunhong-7 cultivar by combining PacBio and Hi-C technologies. Through comparative genomic analysis, we identified structural variations (SVs) between yunhong-7 and anhui-1, which revealed their genetic differences in the pathways of fatty acid biosynthesis, circadian rhythm and flavonoid biosynthesis. Subsequently, a total of 40 non-redundant fatty acid desaturase 2 (FAD2) genes (39 for yunhong-7 and 20 for anhui-1) were identified, revealing the presence of copy-number variation and major genes change between yunhong-7 and anhui-1. The presented results suggested that changes in SVs may induce alterations in the expression of flowering-related genes, which could explain the observed early flowering phenotype in yunhong-7 compared to anhui-1. We identified a total of 197 non-redundant UDP-glucuronosyltransferases (UGT) genes. Based on prokaryotic expression system, we investigated the catalytic functions of two unique UGT genes (CtUGT.18 and CtUGT.191). The current study increases our knowledge of genetic diversity among crop cultivars resulting from distinct domestication processes and thus could contribute to the advancement of traits research and the safflower breeding.

Structural variation-based and gene-based pangenome construction reveals untapped diversity of hexaploid wheat

Increasing number of structural variations (SVs) have been identified as causative mutations for diverse agronomic traits. However, the systematic exploration of SVs quantity, distribution, and contribution in wheat was lacking. Here, we report high-quality gene-based and SV-based pangenomes comprising 22 hexaploid wheat assemblies showing a wide range of chromosome size, gene number, and TE component, which indicates their representativeness of wheat genetic diversity. Pan-gene analyses uncover 140,261 distinct gene families, of which only 23.2 % are shared in all accessions. Moreover, we build a ∼16.15 Gb graph pangenome containing 695,897 bubbles, intersecting 5132 genes and 230,307 cis-regulatory regions. Pairwise genome comparisons identify ∼1,978,221 non-redundant SVs and 497 SV hotspots. Notably, the density of bubbles as well as SVs show remarkable aggregation in centromeres, which probably play an important role in chromosome plasticity and stability. As for functional SVs exploration, we identify 2769 SVs with absolute relative frequency differences exceeding 0.7 between spring and winter growth habit groups. Additionally, several reported functional genes in wheat display complex structural graphs, for example, PPD-A1, VRT-A2, and TaNAAT2-A. These findings deepen our understanding of wheat genetic diversity, providing valuable graphical pangenome and variation resources to improve the efficiency of genome-wide association mapping in wheat.

Super pan-genome reveals extensive genomic variations associated with phenotypic divergence in Actinidia

Kiwifruit is an economically and nutritionally important horticultural fruit crop worldwide. The genomic data of several kiwifruit species have been released, providing an unprecedented opportunity for pan-genome analysis to comprehensively investigate the inter- and intra-species genetic diversity and facilitate utilization for kiwifruit breeding. Here, we generated a kiwifruit super pan-genome using 15 high-quality assemblies of eight Actinidia species. For gene-based pan-genome, a total of 61,465 gene families were identified, and the softcore and dispensable genes were enriched in biological processes like response to endogenous stimulus, response to hormone and cell wall organization or biogenesis. Then, structural variations (SVs) against A. chinensis 'Donghong' were identified and then used to construct a graph-based genome. Further population-scale SVs based on resequencing data from 112 individuals of 20 species revealed extensive SVs which probably contributed to the phenotypic diversity among the Actinidia species. SV hotspot regions were found contributed to environmental adaptation. Furthermore, we systematically identified resistance gene analogs (RGAs) in the 15 assemblies and generated a pan-RGA dataset to reveal the diversity of genes potentially involved in disease resistance in Actinidia. The pan-genomic data obtained here is useful for evolutionary and functional genomic studies in Actinidia, and facilitates breeding design.

The era of panomics-driven gene discovery in plants

Panomics is an approach to integrate multiple 'omics' datasets, generated using different individuals or natural variations. Considering their diverse phenotypic spectrum, the phenome is inherently associated with panomics-based science, which is further combined with genomics, transcriptomics, metabolomics, and other omics techniques, either independently or collectively. Panomics has been accelerated through recent technological advancements in the field of genomics that enable the detection of population-wide structural variations (SVs) and hence offer unprecedented insights into the genetic variations contributing to important agronomic traits. The present review provides the recent trends of panomics-driven gene discovery toward various traits related to plant development, stress tolerance, accumulation of specialized metabolites, and domestication/dedomestication. In addition, the success stories are highlighted in the broader context of enhancing crop productivity.

A wild melon reference genome provides novel insights into the domestication of a key gene responsible for melon fruit acidity

KEY MESSAGE

A wild melon reference genome elucidates the genomic basis of fruit acidity domestication. Structural variants (SVs) have been reported to impose major effects on agronomic traits, representing a significant contributor to crop domestication. However, the landscape of SVs between wild and cultivated melons is elusive and how SVs have contributed to melon domestication remains largely unexplored. Here, we report a 379-Mb chromosome-scale genome of a wild progenitor melon accession "P84", with a contig N50 of 14.9 Mb. Genome comparison identifies 10,589 SVs between P84 and four cultivated melons with 6937 not characterized in previously analysis of 25 melon genome sequences. Furthermore, the population-scale genotyping of these SVs was determined in 1175 accessions, and 18 GWAS signals including fruit acidity, fruit length, fruit weight, fruit color and sex determination were detected. Based on these genotyped SVs, we identified 3317 highly diverged SVs between wild and cultivated melons, which could be the potential SVs associated with domestication-related traits. Furthermore, we identify novel SVs affecting fruit acidity and proposed the diverged evolutionary trajectories of CmPH, a key regulator of melon fruit acidity, during domestication and selection of different populations. These results will offer valuable resources for genomic studies and genetic improvement in melon.

Crop Landraces and Indigenous Varieties: A Valuable Source of Genes for Plant Breeding

Landraces and indigenous varieties comprise valuable sources of crop species diversity. Their utilization in plant breeding may lead to increased yield and enhanced quality traits, as well as resilience to various abiotic and biotic stresses. Recently, new approaches based on the rapid advancement of genomic technologies such as deciphering of pangenomes, multi-omics tools, marker-assisted selection (MAS), genome-wide association studies (GWAS), and CRISPR/Cas9 gene editing greatly facilitated the exploitation of landraces in modern plant breeding. In this paper, we present a comprehensive overview of the implementation of new genomic technologies and highlight their importance in pinpointing the genetic basis of desirable traits in landraces and indigenous varieties of annual, perennial herbaceous, and woody crop species cultivated in the Mediterranean region. The need for further employment of advanced -omic technologies to unravel the full potential of landraces and indigenous varieties underutilized genetic diversity is also indicated. Ultimately, the large amount of genomic data emerging from the investigation of landraces and indigenous varieties reveals their potential as a source of valuable genes and traits for breeding. The role of landraces and indigenous varieties in mitigating the ongoing risks posed by climate change in agriculture and food security is also highlighted.