Genomic conservation of crop wild relatives: A case study of citrus

Abstract

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.

Comparative population genomics reveals convergent and divergent selection in the apricot–peach–plum–mei complex

“…purifying selection [ 20 ]) effects, both the region itself and neighboring sequences will show reduced genetic diversity. Selective sweeps identified in domesticated populations, including maize [ 21 ], cattle [ 22 ], grapes [ 23 ], and citrus [ 24 ], have enhanced our understanding of genetic architecture and artificial selection during the domestication history of agronomic traits [ 25 , 26 ].…”

Integrative genomics reveals the polygenic basis of seedlessness in grapevine

“…To distinguish convergent selection and introgression in generating seedless traits in different grapevine lineages, we preformed the introgression analyses, throughout the whole genome using f d statistics 53 , following previous studies 54,55 . Interestingly, we detected significant genomic signals of introgression at seedless associated locus (see the GWAS section) between VV and VV×VL seedless grapes (the upper 5th percentile, f d = 0.266, P = 1.28e-39), including the redefined SEED DEVELOPMENT INHIBITOR (SDInew, 30.36-31.86 Mb) locus 20 and the newly detected QTL on Chr07 (SDI2, 8.85-8.86 Mb; Fig.…”