Molecular characterization of Asian maize inbred lines by multiple laboratories

Abstract

This study focuses on the standardization of techniques across laboratories to enable multiple datasets to be compared and combined in order to obtain reliable and robust wide-scale patterns of diversity. A set of protocols using a core collection of simple sequence repeat (SSR) markers, reference lines and standard alleles, plus a common system of allele nomenclature, was adopted in the study of maize genetic diversity in a network of laboratories in Asia. Pair-wise allele comparisons of the reference lines, done to assess the general agreement between datasets from four laboratories, showed error rates (raw) ranging from 5.8% to 9.7%, which were reduced to less than 8% after adjustments of correctable errors, and further reduced to less than 6% after the exclusion of all markers with greater than 10% individual error rates. Overall, 45% of the total mismatches were due to frameshift errors, 39% to wrong allele size, 15% to failed amplification and 1% to "extra" alleles. Higher genetic similarity values of the reference lines were achieved using fewer markers with data of higher quality rather than with more markers of questionable quality. Cluster analysis of the merged datasets showed the lines from southern China to be highly diverse, falling into six of the seven clusters observed and all well represented by tester lines. The lines from Indonesia fell into five of six groups, with two main groups represented by tester lines. The CIMMYT lines developed for the Asian region showed a relatively narrow genetic base, falling in two out of seven and in three out of six clusters in China and Indonesia, respectively. In contrast to the case in southern China where 95% of the lines clustered separately from the CIMMYT lines, lines in the Indonesian breeding program show a closer relationship with the CIMMYT lines, reflecting a long history of germplasm exchange.

Molecular diversity and relationships among elite maize inbreds from US and CIMMYT populations and current heterotic groups in China

“…The SSR fragment data were transformed into binary (0/1 for absence/presence of allele) dataset according to the method described by George et al (2004). Polymorphic information content (PIC) value for each locus was estimated according to Smith et al (1997): where f i is the frequency of the i th allele in a locus with k alleles.…”

“…In maize, the high polymorphism of simple sequence repeat (SSR) markers allows us to evaluate genetic diversity (SENIOR and HEUN 1993). SSR markers have been used in numerous studies to assess the genetic diversity and to identify similar or divergent germplasms due to their diverse alleles (SMITH et al 1997;LU and BERNARDO 2001;ENOKI et al 2002;LIU et al 2003;REIF et al 2003;GEORGE et al 2004;XIA et al 2005). DUBREUIL and CHARCOSSET (1999) suggested that molecular marker could provide significant guidelines to select crosses to be tested, although this information was not enough to choose particular genotypes exhibiting high heterotic responses among combinations.…”

A reference microsatellite kit to assess for genetic diversity of Sorghum bicolor (Poaceae)

“…Combining simple sequence repeat (SSR) molecular data obtained from different laboratories or different genotyping platforms is often a challenge, especially for large‐scale analyses and for highly polymorphic markers (for example, George et al, 2004). Although work can be partitioned with markers assigned only to one platform in one laboratory, this is rarely the case.…”

KERAGAMAN GENETIK 22 AKSESI PADI LOKAL TORAJA UTARA BERBASIS MARKA <em>SIMPLE SEQUENCE REPEATS (SSR)</em>

“…Isolasi DNA dilakukan dengan mengikuti prosedur George et al (2004) yang dimodifikasi dengan mengganti nitrogen cair dengan buffer CTAB pada saat penggerusan jaringan segar tanaman berdasarkan metode Khan et al (2004).…”