Utility of Selected Non-coding Chloroplast DNA Sequences for Lineage Assessment of Musa Interspecific Hybrids

Abstract

Single-copy chloroplast loci are used widely to infer phylogenetic relationship at different taxonomic levels among various groups of plants. To test the utility of chloroplast loci and to provide additional data applicable to hybrid evolution in Musa, we sequenced two introns, rpl16 and ndhA, and two intergenic spacers, psaA-ycf3 and petA-psbJ-psbL-psbF and combined these data. Using these four regions, Musa acuminata Colla (A)- and M. balbisiana Colla (B)-containing genomes were clearly distinguished. Some triploid interspecific hybrids contain A-type chloroplasts (the AAB/ABB) while others contain B-type chloroplasts (the BBA/BBB). The chloroplasts of all cultivars in 'Namwa' (BBA) group came from the same wild maternal origin, but the specific parents are still unrevealed. Though, average sequence divergences in each region were little (less than 2%), we propose that petA-psbJ intergenic spacer could be developed for diversity assessment within each genome. This segment contains three single nucleotide polymorphisms (SNPs) and two indels which could distinguish diversity within A genome whereas this same region also contains one SNP and an indel which could categorize B genome. However, an inverted repeat region which could form hairpin structure was detected in this spacer and thus was omitted from the analyses due to their incongruence to other regions. Until thoroughly identified in other members of Musaceae and Zingiberales clade, utility of this inverted repeat as phylogenetic marker in these taxa are cautioned.

Genetic variation of Kaempferia (Zingiberaceae) in Thailand based on chloroplast DNA(psbA-trnH and petA-psbJ) sequences

“…However, only one indel at the 5′ end of petA-psbJ was able to further differentiate K. laotica and K. larsenii (excluding TT16540). This indel seems to be a part of the inverted repeat of the stem-loop or hairpin structures commonly found in angiosperms (Kim and Lee, 2004), including Zingiberales (Swangpol et al, 2007). However, external morphology of leaves can be used to unambiguously differentiate K. larsenii and K. laotica.…”

The potential of high-resolution BAC-FISH in banana breeding

“…In recent studies molecular markers were identified for banana classification (Wong et al 2002;Buhariwalla et al 2005;Santos et al 2005;Ruangsuttapha et al 2007;Swangpol et al 2007;Miller et al 2008), but the usefulness of these markers depends on (a) the distribution pattern of the markers on the chromosomes; (b) the genetic and structural location of these markers on conserved regions of different genomes; and (c) the possibility of chromosomal rearrangements between potential crossing parents in the chromosome regions of economically important traits (Pillay et al 2004). In order to determine small chromosomal rearrangements such as translocations and inversions or even the position of a smaller DNA sequence a more refined methodology based on single copy fluorescent in situ hybridization (FISH) is required.…”

Molecular and cytological characterization of the global Musa germplasm collection provides insights into the treasure of banana diversity

“…Klutuk' and 'Pisang batu') intermingled with BBs of South Asian origin. Although genetic diversity within M. balbisiana has been reported (Ude et al 2002;Ge et al 2005;Swangpol et al 2007;Wang et al 2007), it is believed that the ITC collection does not cover enough balbisiana diversity to trace the ancestral lineages of triploid cultivars comprising the B-genome (Hippolyte et al 2012).…”