Chromosomal inversions can preserve combinations of favorable alleles by suppressing recombination. Simultaneously, they reduce the effectiveness of purifying selection enabling deleterious alleles to accumulate. This study explores how areas of low recombination, including centromeric regions and chromosomal inversions, contribute to the accumulation of deleterious and favorable loci in 225 Mangifera indica genomes from the Australian Mango Breeding Program. Here, we identify 17 chromosomal inversions that cover 7.7% (29.7 Mb) of the M. indica genome: eight pericentric (inversion includes the centromere) and nine paracentric (inversion is on one arm of the chromosome). Our results show that these large pericentric inversions are accumulating deleterious loci, while the paracentric inversions show deleterious levels above and below the genome wide average. We find that despite their deleterious load, chromosomal inversions contain small effect loci linked to variation in crucial breeding traits. These results indicate that chromosomal inversions have likely facilitated the evolution of key mango breeding traits. Our study has important implications for selective breeding of favorable combinations of alleles in regions of low recombination.

Sexual reproduction in plants is the main pathway for creating new genetic combinations in modern agriculture. In heterozygous plants, after the identification of a plant with desired traits, vegetative propagation (cloning) is the primary path to create genetically uniform plants. Another natural plant mechanism that creates genetically uniform plants (clones) is apomixis. In fruit crops like citrus and mango, sporophytic apomixis results in polyembryony, where seeds contain multiple embryos, one of which is sexually originated and the others are vegetative clones of the parent mother tree. Utilizing the mango genome and genetic analysis of a diverse germplasm collection, we identified MiRWP as the gene that causes polyembryony in mango. There is a strong correlation between a specific insertion in the gene’s promoter region and altered expression in flowers and developing fruitlets, inducing multiple embryos. The MiRWP gene is an ortholog of CitRWP that causes polyembryony in citrus. Based on the data, we speculate that promoter insertion events, which occurred independently in citrus and mango, induced nucellar embryogenesis. The results suggest convergent evolution of polyembryony in the two species. Further work is required to demonstrate the utility of these genes (mango and citrus) in other biological systems as a tool for the clonal production of other crops.

Cotton bunchy top disease causes sporadic but serious losses in cotton ( Gossypium hirsutum ) in Australia but little has been reported about the diversity, distribution, host range and detection of the causal agent, cotton bunchy top virus (CBTV). We have obtained the complete coding sequence of two poleroviruses from symptomatic cotton to cover all seven putative open reading frames. These species are called CBTV-1 and CBTV-2 and all seven predicted gene products differ by 25% to 49% amino acid identity, indicating they are distinct polerovirus species. A multiplex PCR for CBTV-1 and CBTV-2 was used to screen more than 700 plant samples from 36 species to identify 16 new field and experimental host species. Serological detection by tissue blot immune assay was successful when the two viruses were transmitted to chickpea ( Cicer arietinum ), but was unreliable for detecting the viruses in cotton. Volunteer and ratoon cotton were identified as common reservoirs of CBTV nearby to cotton cropping areas. Other species that may be regionally important reservoirs include Malva parviflora , Euphorbia hirta and Gossypium sturtianum . Both CBTV species were common and widespread in all major cotton production regions and the genetic diversity within each species was low for the genome region spanning from the 3’ end of open reading frame (ORF) 2 and complete ORF 3. From a total of 257 cotton plants displaying symptoms typical of cotton bunchy top, 256 (99.6%) were positive for CBTV-2 and 93 of these (36%) were mixed infections of CBTV-2 and CBTV-1. As a single infection, CBTV-1 was non-symptomatic, indicating that CBTV-2 is the causal agent of typical cotton bunchy top disease.

A new polerovirus species with the proposed name faba bean polerovirus 1 (FBPV-1) was found in winter legume crops and weeds in New South Wales, Australia. We describe the complete genome sequence of 5,631 nucleotides, containing all putative open reading frames, from two isolates, one from faba bean (Vicia faba) and one from chickpea (Cicer arietinum). FBPV-1 has a genome organization typical of poleroviruses with six open reading frames. However, recombination analysis strongly supports a recombination event in which the 5′ portion of FBPV-1, which encodes for proteins P0, P1 and P1-P2, appears to be from a novel parent with a closest nucleotide identity of only 66% to chickpea chlorotic stunt virus. The 3′ portion of FBPV-1 encodes for proteins P3, P4 and P3-P5 and shares 94% nucleotide identity to a turnip yellows virus isolate from Western Australia.