Combined bulked segregant sequencing and traditional linkage analysis for identification of candidate gene for purple leaf sheath in maize

Abstract

Anthocyanin accumulation in various maize tissues plays important roles in plant growth and development. In addition, some color-related traits can be used as morphological markers in conventional maize breeding processes and purity identification of hybrid seeds. Here, we noticed that the leaf sheath color was controlled by a dominant gene, because purple (PSH) and green leaf sheaths (GSH) were separated at a ratio of 3:1 in an F2 population. To map the gene, an F2 and a recombinant inbred line (RIL) population were derived from a cross between inbred line T877 (PSH) and DH1M (GSH). The PSH locus was mapped to the genomic region within 128.8 to 138.4 Mb using a bulked segregant sequencing approach. This position was further validated by linkage mapping using 190 F2 plants with GSH. Subsequently, the PSH locus was fine-mapped into an interval of 304.2 kb. A maize gene, GRMZM5G822829, was identified in this region, encoding a bHLH transcription factor. The expression level of this gene in T877 was found to be 9-fold higher than that of DH1M. In conclusion, our results suggest that GRMZM5G822829 is the putative candidate gene conferring leaf sheath color in maize.

Genetics and molecular markers for anthocyanin pigmentation in barnyard millet (Echinochloa frumentacea (Roxb.) Link)

“…This further confirms that the BMESSR 39 marker is closely linked to the gene controlling purple pigmentation in barnyard millet. These results are consistent with the reports of Li et al (2010), Gao et al (2011), andLi et al (2018), who used BSA analysis followed by screening the breeding population to identify the linked markers to anthocyanin/purple pigmentation in wheat, rice and maize, respectively. Furthermore, the validation of BMESSR Furthermore, genetic mapping studies will disclose the precise location of the gene related to anthocyanin pigment in barnyard millet.…”

“…A similar monogenic with the partial dominant inheritance of anthocyanin pigmentation was earlier reported in the pod colour of cowpea (Sangwan & Lodhi, 1998) and curd colour of cauliflower (Chiu et al, 2010; Singh et al., 2020). In contrast, a single gene with dominant expression was also reported for purple inflorescence of wheat (Copp, 1965; Khlestkina, 2013) and rice (Li et al., 2018) and head of the cabbage (Hayashi et al., 2010). Two independent genes controlling the purple‐grain were also reported in wheat (Dobrovolskaya et al., 2006; Li et al., 2010) and rice (Yoshimura et al, 1997) earlier.…”

“…Two independent genes controlling the purple-grain were also reported in wheat (Dobrovolskaya et al, 2006;Li et al, 2010) and rice (Yoshimura et al, 1997) that has long been used in the identification of true hybrids and also as a reporter in transgenic studies in crop plants (Li et al, 2018).…”

“…Anthocyanin pigmentation in plants although plays a pivotal role in defence mechanism, it is the standard visible (phenotype) marker that has long been used in the identification of true hybrids and also as a reporter in transgenic studies in crop plants (Li et al., 2018). However, the development of markers associated with the desired trait will be very useful for shortening the breeding cycle because phenotypic selection requires a very long time from sowing to flowering.…”

Fine mapping and gene cloning in the post-NGS era: advances and prospects

“…Similarly, QTL-Seq approach was applied to fine-map bacterial wilt resistance genes and develop diagnostic markers for use in breeding in the case of groundnut (Luo et al 2019a). Adoption of QTL-Seq is increasingly reported for delineating candidate QTLs for both qualitative and quantitative traits (Yang et al 2017;Li et al 2018;Zhang et al 2018;Clevenger et al 2018;Zhang et al 2019;Luo et al 2019b).…”