Sequence characterization of hypervariable regions in the soybean genome: leucine-rich repeats and simple sequence repeats

Abstract

The genetic basis of cultivated soybean is rather narrow. This observation has been confirmed by analysis of agronomic traits among different genotypes, and more recently by the use of molecular markers. During the construction of an RFLP soybean map (Glycine soja x Glycine max) the two progenitors were analyzed with over 2,000 probes, of which 25% were polymorphic. Among the probes that revealed polymorphisms, a small proportion, about 0.5%, hybridized to regions that were highly polymorphic. Here we report the sequencing and analysis of five of these probes. Three of the five contain segments that encode leucine-rich repeat (LRR) sequence homologous to known disease resistance genes in plants. Two other probes are relatively AT-rich and contain segments of (A)n/(T)n. DNA segments corresponding to one of the probes (A45-10) were amplified from nine soybean genotypes. Partial sequencing of these amplicons suggests that deletions and/or insertions are responsible for the extensive polymorphism observed. We propose that genes encoding LRR proteins and simple sequence repeat region prone to slippage are some of the most hypervariable regions of the soybean genome.<br>A base genética da soja cultivada é relativamente estreita. Essa observação foi confirmada por análises de características agronômicas entre diferentes genótipos e, mais recentemente, pelo uso de marcadores moleculares. Durante a construção de um mapa de RFLP da soja (Glycine soja x Glycine max), os dois progenitores foram analisados com mais de 2000 sondas, das quais 25% eram polimórficas. Entre as sondas que revelaram polimorfismos, uma pequena proporção, cerca de 0,5%, hibridizou com regiões que eram altamente polimórficas. Neste trabalho, são apresentados o seqüenciamento e análise de cinco dessas sondas. Três dessas sondas contêm segmentos que codificam repetições ricas em leucina que são homólogas a genes de resistência a doenças já conhecidos em plantas. As duas outras sondas são relativamente ricas em AT e contêm segmentos do tipo (A)n/(T)n. Segmentos de DNA correspondentes a uma das sondas (A45-10) foram amplificados a partir de nove genótipos de soja. Seqüenciamento parcial desses amplicons sugere que deleções e/ou inserções são responsáveis pelo extensivo polimorfismo observado. Nós propomos que os genes que codificam proteínas com repetições ricas em leucina e regiões de seqüências repetidas simples, que são passíveis do fenômeno de slippage (deslizamento), estão entre as regiões mais variáveis do genoma da soja

Single nucleotide polymorphism, haplotype diversity and recombination in the Isa gene of barley

“…There were, however, no indels and only one SNP in the 139-bp 3′ UTR, although there are anecdotal observations that in general, 3′ UTRs have a higher frequency of polymorphism than coding regions (Bhattramakki et al 2002;Kota et al 2001). A high frequency of SNPs and indels in the region flanking a microsatellite repeat (as observed in the Isa promoter) has also been observed for microsatellite sites in maize (Mogg et al 2002) and soyabean (de Barros et al 2000).…”

Detection of DNA changes in somaclonal mutants of rice using SSR markers and transposon display

“…A similar study by Linacero et al (2000), using RAPD analyses to assess DNA variation of regenerated rye plants, has reported that about 5.2% of scored bands are shared by several regenerated plants derived from different callus. Hypervariable regions (HVR) have also been reported in other organisms, such as soybean, and some HVRs may be related to genes (Barros et al 2000). In human, the tumor-suppressor gene p53 is frequently mutated in different cancers; in addition, the hot spots look different in diverse types of human cancers (Hollstein et al 1991).…”