Abstract
Multi-environment QTL mapping identified 23 stable loci and 34 co-located QTL clusters for panicle architecture and grain yield-related traits, which provide a genetic basis for foxtail millet yield improvement. Panicle architecture and grain weight, both of which are influenced by genetic and environmental factors, have significant effects on grain yield potential. Here, we used a recombinant inbred line (RIL) population of 333 lines of foxtail millet, which were grown in 13 trials with varying environmental conditions, to identify quantitative trait loci (QTL) controlling nine agronomic traits related to panicle architecture and grain yield. We found 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 the 159 QTL, 34 were identified in 2 to 12 environments, suggesting that the genetic control of panicle architecture in foxtail millet is sensitive to photoperiod and/or other environmental factors. Eighty-eight QTL controlling different traits formed 34 co-located QTL clusters, including the triple QTL cluster qPD9.2/qPL9.5/qPEL9.3, which was detected 23 times in 13 environments. Several candidate genes, including Seita.2G388700, Seita.3G136000, Seita.4G185300, Seita.5G241500, Seita.5G243100, Seita.9G281300, and Seita.9G342700, were identified in the genomic intervals of multi-environmental QTL or co-located QTL clusters. Using available phenotypic and genotype data, we conducted haplotype analysis for Seita.2G002300 and Seita.9G064000,which showed high correlations with panicle weight and panicle exsertion length, respectively. These results not only provided a basis for further fine mapping, functional studies and marker-assisted selection of traits related to panicle architecture in foxtail millet, but also provide information for comparative genomics analyses of cereal crops.
Highlights
Foxtail millet (Setaria italica) is one of the most important cereal crops that domesticated in China about 10,000 years ago (Hu et al 2018; Lu et al 2009)
We investigated the foxtail millet phenotypic variations and the broad sense heritability of panicle architecture and grain yield traits of a recombinant inbred line population (RIL) population grown in 13 environments
We found that Panicle weight (PW), grain weight per panicle (GWP), panicle length (PL), and panicle diameter (PD) increased with the increasing latitude (Figure 1)
Summary
Foxtail millet (Setaria italica) is one of the most important cereal crops that domesticated in China about 10,000 years ago (Hu et al 2018; Lu et al 2009). Most of foxtail millet cultivars have only one tiller, which bears one panicle (Doust 2007) Panicle architecture, such as panicle length (PL), panicle diameter (PD), primary branch number (PBN), primary branch length (PBL), and grain number per panicle (GNP) mainly determine grain yield per plant. Gain of function mutations in DENSE AND ERECT PANICLE1 (DEP1) enhance meristematic activity, resulting in a reduced length of the inflorescence internode, and increased number of grains per panicle (Huang et al 2009a). Grain number 1a (Gn1a) encodes a cytokinin oxidase/dehydrogenase (OsCKX2) that degrades cytokinin, loss of function mutations in Gn1a accumulate higher levels of cytokinin in inflorescence meristems, resulting in a larger number of branches and spikelets (Ashikari et al 2005). Due to a KNOX-mediated transcriptional feedback loop, overexpression of Grain Number per Panicle[1] (GNP1), which encodes rice GA20ox[1], increases grain number and yield by increasing cytokinin activity in rice panicle meristems (Wu et al 2016)
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