Fine genetic mapping of the Co locus controlling columnar growth habit in apple

Abstract

Tree architecture is an important, complex and dynamic trait affected by diverse genetic, ontogenetic and environmental factors. 'Wijcik McIntosh', a columnar (reduced branching) sport of 'McIntosh' and a valuable genetic resource, has been used intensively in apple-breeding programs for genetic improvement of tree architecture. The columnar growth habit is primarily controlled by the dominant allele of gene Co (columnar) on linkage group-10. But the Co locus is not well mapped and the Co gene remains unknown. To precisely map the Co locus and to identify candidate genes of Co, a sequence-based approach using both peach and apple genomes was used to develop new markers linked more tightly to Co. Five new simple sequence repeats markers were developed (C1753-3520, C18470-25831, C6536-31519, C7223-38004 and C7629-22009). The first four markers were obtained from apple genomic sequences on chromosome-10, whereas the last (C7629-22009) was from an unanchored apple contig that contains an apple expressed sequence tag CV082943, which was identified through synteny analysis between the peach and apple genomes. Genetic mapping of these five markers in four F(1) populations of 528 genotypes and 290 diverse columnar selections/cultivars (818 genotypes in total) delimited the Co locus in a genetic interval with 0.37 % recombination between markers C1753-3520 and C7629-22009. Marker C18470-25831 co-segregates with Co in the 818 genotypes studied. The Co region is estimated to be 193 kb and contains 26 predicted gene in the 'Golden Delicious' genome. Among the 26 genes, three are putative LATERAL ORGAN BOUNDARIES (LOB) DOMAIN (LBD) containing transcription factor genes known of essential roles in plant lateral organ development, and are therefore considered as strong candidates of Co, designated MdLBD1, MdLBD2, and MdLBD3. Although more comprehensive studies are required to confirm the function of MdLBD1-3, the present work represents an important step forward to better understand the genetic and molecular control of tree architecture in apple.

Tracing a key player in the regulation of plant architecture: the columnar growth habit of apple trees (Malus × domestica)

“…2c). Rarely, the axillary buds do develop into long lateral shoots which then grow almost parallel to the stem at a very narrow crotch angle (Hemmat et al 1997;Bai et al 2012). The development of long side shoots is favored if the central leader is damaged, in which case two to three spurs near the top grow to about 50 cm of length (Tobutt 1985;Watanabe et al 2006), which implicates that the lateral buds are under tight apical control.…”

“…Only crosses with a total plant number higher than 50 and precise numbers of progeny which was not preselected were included. Other research groups reported an approximation of a 1:1 ratio of columnar versus non-columnar individuals without giving precise numbers (Lee and Looney 1978;Hemmat et al 1997;Tian 2005;Zhu et al 2007) a Pooled data from four crosses b Plants grafted on M9 rootstocks at 2 years age c The Telamon 9 Braeburn population used by Bai et al (2012) is the same as the one used by Kenis and Keulemans (2007) Planta (2013) 238:1-22 9…”

“…3a). Bai et al (2012) developed 88 SSR markers based on genomic apple contigs originating from chromosome 10 around the target region as well as from two unanchored contigs which they identified as being located within this region via a synteny approach using the peach genome. They used four segregating progenies as well as 290 columnar selections to evaluate the quality of 18 already published markers and the new SSR markers.…”

“…Marker C18470-25831 (19.0 Mb) was found to co-segregate with Co. The newly delimited region contains 20 annotated genes and 7 predicted genes, 3 of which code for homologs of Lateral Organ Boundaries Domain transcription factors in Arabidopsis (Majer and Hochholdinger 2011) and were thus considered the most likely candidates for Co (Bai et al 2012). Moriya et al (2012) also developed SSR markers based on the Golden Delicious genome sequence and used 1,000 F 1 individuals from 31 populations for linkage analysis.…”

“…Moriya et al (2012) also developed SSR markers based on the Golden Delicious genome sequence and used 1,000 F 1 individuals from 31 populations for linkage analysis. They delimited the Co gene region to 196 kb, a similar size as in Bai et al (2012). However, the markers developed by Moriya et al (2012) Moriya et al (2012), but does not span the chromosomal location predicted for Co by Bai et al (2012).…”