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Conservation of crop wild relatives is critical for plant breeding and food security. The lack of clarity on the genetic factors that lead to endangered status or extinction create difficulties when attempting to develop concrete recommendations for conserving a citrus wild relative: the wild relatives of crops. Here, we evaluate the conservation of wild kumquat (Fortunella hindsii) using genomic, geographical, environmental, and phenotypic data, and forward simulations. Genome resequencing data from 73 accessions from the Fortunella genus were combined to investigate population structure, demography, inbreeding, introgression, and genetic load. Population structure was correlated with reproductive type (i.e., sexual and apomictic) and with a significant differentiation within the sexually reproducing population. The effective population size for one of the sexually reproducing subpopulations has recently declined to ~1,000, resulting in high levels of inbreeding. In particular, we found that 58% of the ecological niche overlapped between wild and cultivated populations and that there was extensive introgression into wild samples from cultivated populations. Interestingly, the introgression pattern and accumulation of genetic load may be influenced by the type of reproduction. In wild apomictic samples, the introgressed regions were primarily heterozygous, and genome-wide deleterious variants were hidden in the heterozygous state. In contrast, wild sexually reproducing samples carried a higher recessive deleterious burden. Furthermore, we also found that sexually reproducing samples were self-incompatible, which prevented the reduction of genetic diversity by selfing. Our population genomic analyses provide specific recommendations for distinct reproductive types and monitoring during conservation. This study highlights the genomic landscape of a wild relative of citrus and provides recommendations for the conservation of crop wild relatives. Author summary: Conservation genomics offers a comprehensive approach to understand the underlying genetic and environmental factors affecting the conservation of species. Despite its importance, the conservation genomics of most crop wild relatives remains poorly understood. In this study, we investigated the population fragmentation, inbreeding, gene flow, and genetic load of a citrus wild relative, Fortunella hindsii, using a combination of genomic, geographical, environmental, and phenotypic data, as well as forward simulations. Fortunella hindsii, listed on the registry of National Key Protected Wild Plants in China, has two types of reproduction, sexual and apomictic. Conservation genomics provided insights into the genetic diversity and structure, which are critical for developing effective conservation strategies. Our analysis also helped to assess the risks of hybridization and introgression from cultivated to wild populations. We found that different patterns of introgression and genetic load may be influenced by reproductive type; for example, deleterious variants may hide in the heterozygous state in apomictic populations. Sexually reproducing samples with the self-incompatibility mechanism can prevent rapid loss of genetic diversity caused by selfing. This study serves as an example of conservation genomics and the importance of utilizing important wild relatives of crops to inform broader conservation efforts. [ABSTRACT FROM AUTHOR]

Interveinal chlorosis in old leaves is a common occurrence in citrus orchards in southern China. The present study investigates the 'Langfeng' navel orange (LF, Citrus sinensis) grafted onto a Trifoliate orange (TO, Poncirus trifoliata) rootstock, which exhibits healthy green leaves, and the 'Newhall' navel orange (NHE, C. sinensis) grafted onto TO, which has typical magnesium (Mg) deficiency-induced chlorosis. Chemical analysis of the rhizosphere soil revealed that the pH values were around 3.92 and that both Mg and calcium (Ca) were significantly deficient in the rhizosphere soil of both grafting combinations (LF/TO and NHE/TO). Furthermore, the chlorotic leaves of NHE/TO had significantly lower levels of Mg, Ca, and phosphorus (P), and the green leaves of NHE/TO had significantly lower levels of Mg and Ca compared to the green leaves of the LF/TO. This suggests that Mg deficiency may be the primary cause of chlorosis in NHE/TO. A greenhouse study using the same graft combinations showed that the LF/TO plants had better growth than the NHE/TO, possibly by promoting Mg uptake and/or improving Mg distribution to leaves, thereby increasing carbon dioxide (CO 2) assimilation and photosynthesis, optimizing carbohydrate distribution, and increasing plant biomass. This results in a phenotype that is tolerant to Mg deficiency. In conclusion, these findings suggest that the LF navel orange could be utilized in the development of new citrus varieties with improved Mg-use efficiency. • Interveinal chlorosis is common in southern China citrus orchards. • Study compares "Langfeng" navel orange (LF) on Trifoliate orange rootstock (TO) to "Newhall" navel orange (NHE) on TO. • Soil analysis showed Mg and Ca deficiencies and NHE/TO had lower levels of Mg, Ca, and P in chlorotic leaves. • Greenhouse study showed better growth in LF/TO plants, indicating improved Mg uptake and tolerance to Mg deficiency. • Findings suggest LF navel orange can be used in new citrus varieties with improved Mg-use efficiency. [ABSTRACT FROM AUTHOR]

The orange subfamily (Aurantioideae) contains several Citrus species cultivated worldwide, such as sweet orange and lemon. The origin of Citrus species has long been debated and less is known about the Aurantioideae. Here, we compiled the genome sequences of 314 accessions, de novo assembled the genomes of 12 species and constructed a graph-based pangenome for Aurantioideae. Our analysis indicates that the ancient Indian Plate is the ancestral area for Citrus-related genera and that South Central China is the primary center of origin of the Citrus genus. We found substantial variations in the sequence and expression of the PH4 gene in Citrus relative to Citrus-related genera. Gene editing and biochemical experiments demonstrate a central role for PH4 in the accumulation of citric acid in citrus fruits. This study provides insights into the origin and evolution of the orange subfamily and a regulatory mechanism underpinning the evolution of fruit taste., (© 2023. The Author(s), under exclusive licence to Springer Nature America, Inc.)

Somatic variations are a major source of genetic diversification in asexual plants, and underpin clonal evolution and the breeding of asexual crops. Sweet orange is a model species for studying somatic variation because it reproduces asexually through apomixis and is propagated asexually through grafting. To dissect the genomic basis of somatic variation, we de novo assembled a reference genome of sweet orange with an average of three gaps per chromosome and a N50 contig of 24.2 Mb, as well as six diploid genomes of somatic mutants of sweet oranges. We then sequenced 114 somatic mutants with an average genome coverage of 41×. Categorization of the somatic variations yielded insights into the single-nucleotide somatic mutations, structural variations and transposable element (TE) transpositions. We detected 877 TE insertions, and found TE insertions in the transporter or its regulatory genes associated with variation in fruit acidity. Comparative genomic analysis of sweet oranges from three diversity centres supported a dispersal from South China to the Mediterranean region and to the Americas. This study provides a global view on the somatic variations, the diversification and dispersal history of sweet orange and a set of candidate genes that will be useful for improving fruit taste and flavour., (© 2021. The Author(s), under exclusive licence to Springer Nature Limited.)