High
yield and superior quality are the main goals pursued by breeders
for crop improvement. However, both of them are complex agronomic
traits controlled by multiple genes, so the simultaneous improvement
of these traits via sexual recombination is time-consuming and direction-uncontrolled.
In this study, to solve this dilemma, we introduced the comparative
genomic analysis based multiplex genome editing system (CG-MGE), a
method for rapid and directional improvement of multiple traits. Application
of this method, association analysis between genotypes and phenotypes
was carried out to mine excellent alleles; subsequently, the rare
excellent alleles of Gn1a, GW2, TGW3, and Chalk5 were simultaneously created
by multiplex genome editing and successfully improved the plant architecture,
grain yield, and quality of a widely cultivated elite rice variety.
Overall, this study provides a method for rapid and directional improvement
of crops, and the application of the CG-MGE will be helpful to accelerate
rational design breeding.
Utilization of resistance (R) genes to breed resistant cultivars is one of the most effective and economical approach to control rice bacterial blight (BB). Xa7, a dominant, broad-spectrum and durable BB-resistant gene, is an ideal gene resource to improve the resistance of rice varieties to bacterial blight, and this well-known gene with important breeding value has been cloned in our recent study. The isolation of Xa7 will facilitate its application in rice breeding by molecular maker-assisted selection (MAS). In this study, based on the specific sequences in the promoter of Xa7, a functional marker, named as MX7, was developed, which can effectively distinguish the dominant BB-resistant Xa7, the recessive BB-susceptible xa7 and the null allele from different rice varieties. Since MX7 is a dominant marker, it can't tell homozygous from heterozygous, a co-dominant marker closely linked to Xa7, named as M6, was developed simultaneously. After verified by amplification in numerous rice varieties and sequence alignment in RICE 3K database, it is proved that marker M6 is co-segregated with the Xa7 locus. In addition, the effectiveness and accuracy of the two markers were further validated by two F2 populations. Finally, the designed makers were effectively applied in MAS breeding to improve the BB-resistance of a susceptible variety. This study not only provides reliable functional markers for the identification of Xa7 gene in different rice materials, but also will contribute to the application of Xa7 gene in marker-assisted selection to breed rice varieties with durable disease resistance.
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