Preferential Disomic Segregation and C. micrantha/C. medica Interspecific Recombination in Tetraploid 'Giant Key' Lime; Outlook for Triploid Lime Breeding.

Dalel Ahmed,Yann Froelicher,Patrick Ollitrault,Franck Curk,Jean Charles Evrard

doi:10.3389/fpls.2020.00939

Abstract

The triploid ‘Tahiti’ lime (C. x latifolia (Yu. Tanaka) Tanaka) naturally originated from a merger between a haploid ovule of lemon (C. x limon (L.) Burm) and a diploid pollen from a ‘Mexican’ lime (C. x aurantiifolia (Christm.) Swing). The very limited natural inter-varietal diversity and gametic sterility of C. latifolia requires a phylogenomic based reconstruction breeding strategy to insure its diversification. We developed a strategy based on interploid hybridization between diploid lemon and the doubled diploid ‘Giant Key’ lime. This lime is a doubled diploid of ‘Mexican’ lime, itself a natural interspecific F1 hybrid between C. medica L. and C. micrantha Wester. For an optimized breeding program, we analyzed the meiotic behavior of the allotetraploid lime, the genetic structure of its diploid gametes, the interspecific recombination between C. medica and C. micrantha, and constructed its genetic map. A population of 272 triploid hybrids was generated using ‘Giant Key’ lime as pollinator. One hundred fifty-eight SNPs diagnostic of C. micrantha, regularly distributed throughout the citrus genome were successfully developed and applied. The genetic structure of the diploid gametes was examined based on C. micrantha doses along the genome. The diploid gametes transmitted in average 91.17% of the parental interspecific C. medica/C. micrantha heterozygosity. Three chromosomes (2, 8, and 9) showed disomic segregation with high preferential pairing values, while the remaining chromosomes showed an intermediate inheritance with a preferential disomic trend. A total of 131 SNPs were assigned to nine linkage groups to construct the genetic map. It spanned 272.8 cM with a low average recombination rate (0.99 cM Mb-1) and high synteny and colinearity with the reference clementine genome. Our results confirmed that an efficient reconstruction breeding strategy for ‘Tahiti’ lime is possible, based on interploid hybridization using a doubled diploid of C. aurantiifolia. The tetraploid parent should be selected for favorable agronomic traits and its genetic value should be efficiently inherited by the progeny thanks to transmission of the high level of parental heterozygosity. However, it would require developing numerous progeny to overcome the linkage drag caused by the limited interspecific recombination associated with the predominant disomic inheritance.

Highlights

In addition to the genitors, some varieties/species were included in the study as controls at the genotype calling step: C. micrantha (ICVN 0101115), ‘Poncire commun’ citron (ICVN 0100701), respectively representative of homozygous genotypes of the C. micrantha and alternative alleles, ‘Mexican’ lime (ICVN 0100140) as heterozygous control with equivalent doses of C. micrantha and alternative alleles (1/1), ‘Tahiti’ lime (ICVN 0100058), and ‘Persian’ lime (ICVN 0101046) as representatives of the C. latifolia triploid lime ideotype, ‘Tanepao’ (ICVN0100836) and ‘Coppenrhad’ (ICVN010838) lime as representative of C. aurantiifolia triploid limes
22 SNPs were selected on chromosome 1 (C1), 24 on C2, 31 on C3, 19 on C4, 19 on C5, 19 on C6, 15 on C7, 17 on C8, and 23 on C9
The 189 sequences were sent to LGC Genomics to develop the primer set; information on the selected diagnostic SNPs of C. micrantha (DSNPs) is provided in Supplementary Table 1

Summary

Introduction

Polyploidy, the state of an organism having more than two paired set of chromosomes, is a major component of angiosperm evolution (Grant, 1981; Otto and Whitton, 2000; Wendel, 2000; Madlung, 2013; Soltis et al, 2015; Alix et al, 2017; Van de Peer et al, 2017) and polyploidization is considered to be the most common sympatric speciation mechanism (Otto and Whitton, 2000; Landis et al, 2018). The benefits of polyploidy in long term evolution have been attributed to different factors, including mutation buffering, increased allelic diversity and heterozygosity, sub- or neo-functionalization of duplicated genes, epigenetic changes, and genome neo-regulation, resulting in phenotypic variation (Comai, 2005; Beest et al, 2012; Madlung, 2013). Interploid hybridization involving diploid and tetraploid parents is a classical breeding approach to diversify these triploid crops

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