Genetic diversity, population structure, and association mapping of biomass traits in maize with simple sequence repeat markers

Abstract

Assessing genetic diversity, population structure, and linkage disequilibrium is important in identifying potential parental lines for breeding programs. In this study, we assessed the genetic and phenotypic variation of 174 normal maize (Zea mays) inbred lines and made association analyses with respect to nine agronomical traits, using 150 simple sequence repeats (SSR). From population structure analysis, the lines were divided into three groups. Association analysis was done with a mixed linear model and a general linear model. Twenty-one marker-trait associations involving 19 SSR markers were observed using the mixed model, with a significance level of P \ 0.01. All of these associations, as well as 120 additional marker-trait associations involving 77 SSR markers, were observed with the general model. Two significant marker-trait associations (SMTAs) were detected at P B 0.0001. In the mixed linear model, one locus was associated with water content, two loci were associated with 100-kernel weight, setted ear length, ear thickness and stem thickness; three loci were associated with ear height, four loci were associated with total kernel weight and five loci were associated with plant height. These results should prove useful to breeders in the selection of parental lines and markers.

Genetic Diversity and Population Structure Among 98 Maize Inbred Lines Investigated With SSR Markers

“…The average polymorphic information content (PIC) value was 0.5067, which was lower than that in Chinese important inbred lines with PIC over 0.6 (Wang et al, 2008;Xie et al, 2008). The number of alleles found in this study is also in agreement with other studies (Wang et al, 2008;Park et al, 2015 average of 9.4 alleles per locus by screening 95 inbred lines using SSR markers. Park et al (2015) genotyped 174 maize inbred lines by 150 SSR markers and detected a total of 1082 alleles with an average of 7.21 alleles per locus.…”

Establishment and confirmation of heterotic groups and genetic diversity assessment of maize inbred lines using microsatellite data

“…The rest of them a reasonably informative with a PIC value between 0.30 and 0.50. DEMISSEW et al (2015) reported similar average value for PIC (0.491), athough greater values were presented in other studies (REID et al 2011;PARK et al, 2015). One third of molecular markers used were with dinuocleotide repeats but relatively low PIC detected could be caused by high level of genetic similarity among analyzed genotypes.…”

Genetic variation of growth dynamics in maize (Zea mays L.) revealed through automated non‐invasive phenotyping

“…However, because many QTL analyses performed using linkage mapping (e.g. involving RIL or DH populations) result in large QTL confidence intervals (Messmer et al, 2009;Hao et al, 2010;Li et al, 2010;Almeida et al, 2013;Penning et al, 2014;Park et al, 2015) and the respective individual linkage maps may vary greatly (Semagn et al, 2013), relatively wide chromosomal segments have to be considered and such co-locations have thus to be regarded as tentative. Nevertheless, Peiffer et al (2014) showed that the strongest GWAS associations were often located near the most robust family-nested QTL.…”

“…Among the 35, 22 and 35 top height-associated QTL/QTN detected through joint linkage mapping of QTL, joint-linkage-assisted GWAS across RILs, and GWAS in the NCRPIS panel, respectively, five of the 16 marker loci detected in the present study (SYN7010, SYN7969, PZE-106047590, PZE-106105143, SYN22194) had matching positions. One of these positions also relates to a QTL region for plant height detected by Park et al (2015). Three of the markers (SYN7010, SYN7969, PZE-106105143) and two other markers (PZE-109041871; PZE-110073407) also coincided with QTL affecting maize grain yield (Messmer et al, 2009;Hao et al, 2010;Li et al, 2010;Almeida et al, 2013), and the latter of the two markers (PZE-110073407) is also located near QTL positions for drought tolerance index (Guo et al, 2008) and for drought and low nitrogen tolerance (Malosetti et al, 2008).…”