Genetic control and phenotypic characterization of panicle architecture and grain yield-related traits in foxtail millet (Setaria italica)

Abstract

Panicle architecture and grain weight, both of which are in uenced by genetic and environmental factors, have signi cant effects on grain yield potential. Here, we used a recombinant inbred line population (RIL) of 333 lines, which were grown in 13 trials with varying environmental conditions, to identify quantitative trait loci (QTL) that control differences in 9 agronomic traits related to panicle architecture and grain yield.We nd that panicle weight, grain weight per panicle, panicle length, panicle diameter, and panicle exsertion length varied across different geographical locations. QTL mapping revealed 159 QTL for nine traits, of these, 34 QTL were identi ed in 2 to 12 environments, suggesting that the genetic control of panicle architecture in foxtail millet is sensitive to photoperiod or other environmental factors. 88 QTL controlling different traits formed 34 co-located QTL clusters, including the triple QTL cluster qPD9.2/qPL9.5/qPEL9.3, the genomic region of which was detected by 23 times in 13 environments. Several candidate genes were identi ed in the genomic intervals of multi-environmental QTL or colocated QTL clusters, including Seita.2G388700, Seita.3G136000, Seita.4G185300, Seita.5G241500, Seita.5G243100, Seita.9G281300, and Seita.9G342700. Among these, Seita.9G342700 was the candidate gene of qPD9.2/qPL9.5/qPEL9.3 QTL cluster, it is homologous to rice OsMADS56, which encodes a putative MADS-box transcription factor that determines inflorescence architecture in rice. These results not only provided a basis for further ne mapping, functional studies and marker-assisted selection of panicle architecture related traits in foxtail millet, but also bene ted comparative genomics of cereal crops.

Genome-wide identification of quantitative trait loci for morpho-agronomic and yield-related traits in foxtail millet (Setaria italica) across multi-environments

“…Furthermore, QTL for some negatively correlated traits, such as qSD9.1 and qGNS9.1, belonged to the same cluster 9.2. These results indicate that there was a presence of genetic linkage or pleiotropy effects among traits with significant correlation (Fang et al 2016 ; Zhi et al 2021 ).…”

“…The QTL cluster was defined as a chromosome region harboring multiple QTL for various traits within ~ 20 cM (Tan et al 2018 ). And phenotypically correlated traits are often mapped to similar genomic regions (Zhi et al 2021 ). Of 221 QTL for seventeen traits, 130 with overlapping intervals formed 22 QTL clusters (Table 2 ).…”

“…In foxtail millet, Zhang et al ( 2017 ) positioned the QTL for PL, FLL, and PH that all clustered on the chromosomes 5 and 9. Zhi et al ( 2021 ) identified 34 co-located QTL clusters involving nine traits related to panicle architecture and grain yield. Wang et al ( 2019b ) suggested that intercorrelated traits were probably associated with the growth module and genetic regulation pathway.…”

“…Among the 26 QTL for plant height identified by He et al ( 2021 ), the dwarfing favorable alleles of 8 QTL came from the parent with higher plant height. Zhi et al ( 2021 ) identified 159 QTL for panicle architecture and grain yield-related traits, of which the additive effects of 60 QTL were from Ai88 and the additive effects of 89 QTL were from Liaogu1. In the present study, the 74 and 147 QTL alleles increasing phenotypic values originated from Longgu7 and Yugu1, respectively.…”

The Integration of Genome-Wide Association Study and Homology Analysis to Explore the Genomic Regions and Candidate Genes for Panicle-Related Traits in Foxtail Millet

“…Most of these studies were based on a small number of polymorphic loci, and fewer QTL were identified. A recent QTL mapping study based on 12 environments identified 159 QTLs associated with panicle-related traits, which improved our understanding of the genetic basis for panicle and yield formation in foxtail millet [ 17 ]. However, QTL results based on bi-parental populations are heavily dependent on the genetic background of the population and environment, which greatly limits the wide adaptability and stability of these QTLs in foxtail millet breeding programs [ 18 ].…”