Dissecting the Genetic Basis of Lateral and Central Spikelet Development and Grain Traits in Intermedium-Spike Barley (Hordeum vulgare Convar. Intermedium).

Helmy M Youssef,Martin Mascher,Faiza Boussora,Sara G Milner,Axel Himmelbach,Mohamed Allam,Thorsten Schnurbusch

doi:10.3390/plants9121655

Abstract

Barley (Hordeum vulgare L.) is one of the major grain crops worldwide and considered as a model plant for temperate cereals. One of the barley row-type groups, named intermedium-barley, was used in our previous study where we reported that other genetic loci rather than vrs1 and Int-c could play a role in lateral spikelet development and even in setting grains. To continue this work, we used phenotypic and genotypic data of 254 intermedium-spike barley accessions aimed at dissecting the genetic basis of development and grain traits of lateral and central spikelet using genome wide association (GWAS) analysis. After genotypic data filtering, 8,653 single-nucleotide polymorphism (SNPs) were used for GWAS analysis. A total of 169 significant associations were identified and we focused only on the subset of associations that exceeded the p < 10−4 threshold. Thirty-three highly significant marker-trait-associations (MTAs), represented in 28 different SNPs on all seven chromosomes for the central and/or lateral spikelet traits; such as kernel length, width, area, weight, unfilled spikelet and 1000-kernel weight, were detected. Highly significant associated markers were anchored physically using barley genome sequencing to identify candidate genes to either contain the SNPs or the closest gene to the SNP position. The results showed that 12 MTAs were specific for lateral spikelet traits, nine MTAs were specific for central spikelet traits and seven MTAs for both central and lateral traits. All together, the GWAS and candidate gene results support our hypothesis that lateral spikelet development could be regulated by loci different from those regulating central spikelet development.

Highlights

Barley (Hordeum vulgare L.) is one of the most highly produced and consumed grains in the world, classified as the fourth major cereal crop globally [1]
These results suggested that other genetic loci or allelic combinations could play a role in lateral spikelet development and even in setting grains
We focused on a better understanding of the spikelet development and its effects on barley grain production

Summary

Introduction

Barley (Hordeum vulgare L.) is one of the most highly produced and consumed grains in the world, classified as the fourth major cereal crop globally [1]. It is an excellent experimental model for other cereals, due to its simple inbreeding and diploid genome. Plants 2020, 9, 1655 consists of three single-flowered spikelets—one central and two lateral spikelets per rachis node—that confer unique row-type identity to barley spikes. Disabling sterility in the lateral florets seems a straightforward way to triple the number of grains at each rachis node, that was the route of six-rowed barley to arose from the ancestral two-rowed barley. The intermedium-barley might be a transition form from two- to six-rowed barley

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