Genetic Analysis in Maize Foundation Parents with Mapping Population and Testcross Population: Ye478 Carried More Favorable Alleles and Using QTL Information Could Improve Foundation Parents

Abstract

The development of maize foundation parents is an important part of genetics and breeding research, and applying new genetic information to produce foundation parents has been challenging. In this study, we focused on quantitative trait loci (QTLs) and general combining ability (GCA) of Ye478, a widely used foundation parent in China. We developed three sets of populations for QTL mapping and to analyze the GCA for some agronomic traits. The assessment of 15 traits resulted in the detection of 251 QTLs in six tested environments, with 119 QTLs identified through a joint analysis across all environments. Further, analyses revealed that most favorable alleles for plant type-related traits were from Ye478, and more than half of the favorable alleles for yield-related traits were from R08, another foundation parent used in southwestern China, suggesting that different types of foundation parents carried different favorable alleles. We observed that the GCA for most traits (e.g., plant height and 100-kernel weight) was maintained in the inbred lines descended from the foundation parents. Additionally, the continuous improvement in the GCA of the descendants of the foundation parents was consistent with the main trend in maize breeding programs. We identified three significant genomic regions that were highly conserved in three Ye478 descendants, including the stable QTL for plant height. The GCA for the traits in the F7 generation revealed that the QTLs for the given traits per se were affected by additive effects in the same way in different populations.

Quantitative trait loci mapping for yield‐related traits under low and high planting densities in maize (Zea mays)

“…QC9‐1 had an effect on CWPE (LD), CD (LD, HD) and ED (HD), co‐mapped with QJCD9 for CD in the F 2:3 families from the same parents (Liu et al, ) and MQTL‐63 for grain yield, ear‐related traits and kernel‐related traits reported by Chen et al (). Moreover, QC9‐2 for ED and RN under low density was found in the F 2:3 generation from the same cross (Liu et al, ). The hotspot region QC3‐3 being particularly interesting was associated with up to nine traits, and this region also affected the heterosis for yield‐related traits (Yi, Liu, et al, ), suggesting that the pleiotropic region is of importance for grain yield.…”

“…Quantitative trait loci pleiotropy has been widely reported by many studies (Guo et al, ; Hou et al, ; Liu et al, ). Here, 26 QTL clusters integrated with 69 QTLs for yield‐related traits.…”

“…Two QTLs at bin 5.04 shared the genomic region (QC5) for EL and KNPR across both densities, and this locus also overlapped with a pleiotropic region for EL and CWPE across low and high densities, RN under low density and KNPR under high density according to Guo et al (). The cluster QC3‐1 for KW and RN under high planting density and QJRN3 for RN in the F 2:3 families derived from the same cross were mapped in the same position (Liu et al, ), and this cluster also co‐located with the genomic region that affected CWPE and ED under low‐ and high‐density conditions (Guo et al, ). QC9‐1 had an effect on CWPE (LD), CD (LD, HD) and ED (HD), co‐mapped with QJCD9 for CD in the F 2:3 families from the same parents (Liu et al, ) and MQTL‐63 for grain yield, ear‐related traits and kernel‐related traits reported by Chen et al ().…”

“…The cluster QC3‐1 for KW and RN under high planting density and QJRN3 for RN in the F 2:3 families derived from the same cross were mapped in the same position (Liu et al, ), and this cluster also co‐located with the genomic region that affected CWPE and ED under low‐ and high‐density conditions (Guo et al, ). QC9‐1 had an effect on CWPE (LD), CD (LD, HD) and ED (HD), co‐mapped with QJCD9 for CD in the F 2:3 families from the same parents (Liu et al, ) and MQTL‐63 for grain yield, ear‐related traits and kernel‐related traits reported by Chen et al (). Moreover, QC9‐2 for ED and RN under low density was found in the F 2:3 generation from the same cross (Liu et al, ).…”

Divergence among maize genotypes with different kernel types according to SSR marker analysis

“…These alleles could be successffuly used in new breeding programs for making improved maize hybrid varieties (MESEKA et al, 2015). Moreover, for a hybrid with good performances, an adequate combination of parental components is also necessary (LIU et al, 2016). Thus, thorough examination of genetic diversity stands as the indispensable step at the beginning of a new breeding program process.…”