Trait variation and genetic diversity in a banana genomic selection training population.

Moses Nyine,Allan Brown,Michael Batte,Brigitte Uwimana,Jaroslav Doležel,Pavla Christelová,Rony Swennen,Jim Lorenzen,Eva Hřibová,Marco Buenrostro-Nava

doi:10.1371/journal.pone.0178734

Abstract

Banana (Musa spp.) is an important crop in the African Great Lakes region in terms of income and food security, with the highest per capita consumption worldwide. Pests, diseases and climate change hamper sustainable production of bananas. New breeding tools with increased crossbreeding efficiency are being investigated to breed for resistant, high yielding hybrids of East African Highland banana (EAHB). These include genomic selection (GS), which will benefit breeding through increased genetic gain per unit time. Understanding trait variation and the correlation among economically important traits is an essential first step in the development and selection of suitable GS models for banana. In this study, we tested the hypothesis that trait variations in bananas are not affected by cross combination, cycle, field management and their interaction with genotype. A training population created using EAHB breeding material and its progeny was phenotyped in two contrasting conditions. A high level of correlation among vegetative and yield related traits was observed. Therefore, genomic selection models could be developed for traits that are easily measured. It is likely that the predictive ability of traits that are difficult to phenotype will be similar to less difficult traits they are highly correlated with. Genotype response to cycle and field management practices varied greatly with respect to traits. Yield related traits accounted for 31–35% of principal component variation under low and high input field management conditions. Resistance to Black Sigatoka was stable across cycles but varied under different field management depending on the genotype. The best cross combination was 1201K-1xSH3217 based on selection response (R) of hybrids. Genotyping using simple sequence repeat (SSR) markers revealed that the training population was genetically diverse, reflecting a complex pedigree background, which was mostly influenced by the male parents.

Highlights

East Africa is considered a secondary center of banana genetic diversity
A positive and significant correlation was observed between bunch weight at full maturity (BWT) and all fruit traits (NH, number of fruit fingers (NF), fruit length (FL), fruit circumference (FC), fruit diameter (FRD), pulp diameter (PLD)), which were significantly and positively correlated to each other
The largest proportion of genetic variation was due to the greater genetic diversity of male parents used in crosses since the tetraploids used in the majority of crosses as female parents were genetically related

Summary

Introduction

Uganda in particular is a home to over eighty cultivars of East African Highland banana (EAHB) commonly divided into cooking and beer types [1]. Sustainable production of bananas is a challenge because of disease, insect and nematode pressure. This is worsened by abiotic stress arising through factors associated with climate change [5]. Yield reductions in EAHB are caused by pests such as root burrowing nematodes especially Radopholus similis and banana weevil (Cosmopolites sordidus). Musacearum causes 100% yield loss when the banana is attacked [6,7,8]. Variation in rainfall patterns impacts banana production by causing drought stress because most farmers in the region rely on rain for agricultural production. Adaptation of cultivated banana varieties to changing environment is limited because while some are capable of sexual reproduction, they are all propagated clonally

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Discussion

Conclusion