Genetic characterization of rainfed upland New Rice for Africa (NERICA) varieties

Abstract

A total of 18 rainfed upland New Rice for Africa (NERICA) varieties were categorized as the heavy panicle and low tillering types and early heading, in compared with 32 different varieties. These chromosome components were clarified using 243 SSR markers which showed polymorphism among NERICA varieties and their parents, CG 14 (O. glaberrima Steud.) and one of the recurrent parents, WAB-56-104 (O. sativa L.). NERICA varieties were classified into three groups, which corresponded with these parents' continuation including two exceptions, NERICAs 14 and 17, by a cluster analysis using polymorphism data of SSR markers and 14 differential markers among them were selected to classify NERICA varieties. However, three groups: NERICAs, 3 and 4, NERICAs, 8, 9 and 11 and NERICAs, 15 and 16 were not distinguishable. Association analysis was carried out for characterization of NERICA varieties by using SSR markers genotype and phenotype of agronomic traits. A total of 131 quantitative trait loci between SSR markers and 11 agronomic traits were detected. The characteristics of early maturity and heavy panicle of upland NERICA varieties were succeeded from Asian rice varieties and the characteristics of high dry matter production and late heading were introduced from CG 14 and the other varieties.

Keywords: O. glaberrima Steud.; chromosome introgression; rainfed upland NERICA; rice (Oryza sativa L.); yield components.

Fig. 1

Variation of upland NERICA varieties for agronomic traits in compared with the 32 controls. Black and white arrows indicate the averages of 18 upland NERICA and the other 32 varieties, respectively.

Fig. 2

Classification of 18 upland NERICA varieties. Cluster analyses were carried out with genotype data of 243 SSR markers and nine agronomic traits following Ward’s hierarchal analysis (Ward 1963) using JMP6.0 software (SAS Institute Inc., Cary, NC, USA) for Windows in each. “a” and “b” indicate cluster analyses for agronomic traits and genotype of SSR markers, respectively. A total 50 varieties including 18 upland NERICAs were classified into 5 groups, A–E based on the cluster analysis for agronomic traits. A total 22 varieties unclosing CG 14, Kasalath, Nippaonbare, WAB 56-104 and 18 NERICAs were classified into six groups, I–VI. Dashed lines indicate position of Nipponbare and Kasalath.

Fig. 3

Frequencies of SSR markers showed different polymorphism patterns form WAB 56-104 of upland NERICA varieties in each chromosome. Arrows indicate the means of 18 upland NERICAs. Dotted lines indicate the theoretical frequency, 12.5%, of different polymorphism markers in the progenies derived from the two times’ backcrossing by recurrent parents, WAB-56-104.

Fig. 4

Differential markers for the 18 upland NERICA varieties and its capability of differentiation. A: WAB 56-104 type, B: CG 14 type, C: Other types. Polymorphism patterns enclosed by a heavy line are the unique pattern to differentiate NERICA varieties. Superior numbers indicates the number of upland NERICA varieties showing specific polymorphic pattern. Three variety groups of two NERICAs, 3 and 4, three NERICAs, 8, 9 and 11 and two NERICAs, 15 and 16, were not differentiated from each other in the same groups.

Fig. 5

Association analysis between SSR markers and agronomic traits in 18 NERICA varieties. Thick bars on chromosomes were regions showing the different polymorphism patterns from WAB 56-104 among 18 NERICAs. SSR markers associated with agronomic traits are indicated with underlines. ANOVA test were carried out between traits’ values of WAB 56-104 and the other including CG-14 genotype at 1% significant level. The F values are indicated the combination between association markers and traits in each chromosome’s right side. Minus and plus of F indicate the increasing and decreasing of the values of traits with the other including CG-14 genotype, respectively. PN: Panicle No., DTH: Days to heading, CW: Culm and leaves weight, PW: Panicle weight, TW: Total weight of panicle, culm and leaves, CL: Culm length, PL: Panicle length, TL: Total length, RFS: Ratio of fertility seeds per panicle, SN: Spikelet No. per panicle, RPC: Ratio of panicle against culm and leaves’ weights.