Genomic insights into historical improvement of heterotic groups during modern hybrid maize breeding

A Common Resequencing-Based Genetic Marker Dataset for Global Maize Diversity

“…However, it should be emphasized that HapMap3 utilized a different variant calling pipeline and that the median sequencing depth of samples in that study was ∼2x. A more recent study that examined the genetic differentiation of male and female heterotic groups in maize using resequencing data from 1,604 maize inbred lines, primarily from China and the USA, resequenced to an average depth of ∼7.5x identified ∼242 million DNA sequence polymorphisms (Li et al ., 2022).…”

“…A recent literature study identified more than 160 distinct trait datasets scored across North American temperate maize association panels between 2010 and 2020 (Mural et al ., 2022). During the past seventeen years, the density of publicly available markers for maize association panels has grown from 94 microsatellite markers (Flint-Garcia et al ., 2005) to 1,536 microarray-based SNP markers (Hansey et al ., 2011) to hundreds of thousands of markers scored using genotyping by sequencing (Romay et al ., 2013) and approximately one million markers scored using RNA-seq (Leiboff et al ., 2015; Mazaheri et al ., 2019) and now typically include tens of millions of markers discovered and scored via whole genome resequencing (Bukowski et al ., 2018; Chen et al ., 2022; Li et al ., 2022; Qiu et al ., 2021; Wang et al ., 2020) or a combination of whole genome resequencing for a subset of lines and imputation from lower density markers for additional lines (Mural et al ., 2022; Sun et al ., 2022).…”

Identification of a new QTL underlying seminal root number in a maize-teosinte population

“…RNA-Seq has become an effective technology to detect expressed genes related to development and growth traits in maize, such as kernel development ( Li et al., 2022 ) and drought tolerance ( Liu et al., 2020 ). To our knowledge, there have been few RNA-Seq studies on seminal root primordia, which ultimately determine the number of seminal roots.…”

“…mexicana (CIMMYT accession number 249743). In addition, an association panel including 351 elite inbred lines derived from a large association mapping population ( Li et al., 2022 ) was used to conduct regional association mapping.…”

“…The genotype data from the association panel of 351 inbred lines in the qSRN7 interval were extracted from the resequencing data of 1,604 maize inbred lines reported by Li et al. (2022) .…”