PONE-D-21-23112

Genetic diversity of local and introduced cassava germplasm in Burundi using DArTseq molecular analyses

PLOS ONE

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PLOS ONE

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[This work was sponsored by the International Institute of Tropical Agriculture (IITA) under the ‘CBSD (Cassava Brown Streak Disease) Control Project’. The project is funded by the International Fund for Agricultural Development (IFAD) and the “Institut des Sciences Agronomiques du Burundi” (ISABU) is the main partner in Burundi. The cassava research team from ISABU are acknowledged for their support in trial management and data collection. Ms Chepkoech, Jackline, a laboratory technician at the Integrated Genotyping Service and Support (IGSS) of the Bioscience Eastern and Central Africa supported the molecular analysis work.]

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Additional Editor Comments:

Reviewers have found your manuscript interesting for consideration in PLOS ONE, however they have made some suggestions which need to be incorporated before it can be accepted for publication.

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Reviewers' comments:

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Reviewer #1: Yes

Reviewer #2: Yes

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #1: Yes

Reviewer #2: Yes

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5. Review Comments to the Author

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Reviewer #1: The research paper presents an analysis of the diversity in cassava landraces in Barundi. Overall, the manuscript is well written, and provides insight into the morphological and molecular diversity present in the cassava germplasm of Barundi. The experiments are well planned and executed and after analysis, some important conclusions have been arrived upon which can be utilized for designing further strategies for improvement of this plant species. However, some suggestions are enlisted below:

1. In the abstract the authors mention that the study is aimed at developing a core set of cassava germplasm from the local varieties (Line 30), however no mention of this objective is made in the manuscript text, nor has any analysis been done to this end. The manuscript deals with the genetic diversity present in the landraces and elite lines. Appropriate corrections may be incorporated in the abstract.

2. Discussion on molecular characterization and duplicate identification may elaborated.

3. Overall, the discussion section may be improved.

4. Cassava plants were planted in two locations. Did the authors observe any morphological variation among the same plants at the two locations? If yes, authors could indicate the effect of the environment/ soil etc. on the morphological characteristics.

5. Authors have studied cassava landraces from four different sites along with elite introduced germplasm. Can they carry out a population structure analysis for the four different populations and present it graphically? The analysis may bring out important information on the extent of mixing that may have happened in these genotypes over the course of time.

6. Authors may also support/depict the genetic diversity and genetic classifications they have observed using Principal Component Analysis (PCA).

7. Sentence framing and language may be checked in some parts of the introduction and discussion.

Reviewer #2: The MS “Genetic diversity of local and introduced cassava germplasm in Burundi using DArTseq molecular analyses” presents the results of original research and experiment for morphological and DArT marker analyses and statistics have been performed for assessment of cassava genetic resources in Burundi in sufficient detail.

ALthough, authors may consider the following comment for improvement of the manuscript. Diversity Arrays Technology is a high-throughput genotyping method for preferential sampling of gene-rich regions that is achieved through the use of methylation sensitive restriction enzymes. The authors must use the DArT markers to perform redundancy analysis and assemble the non-redundant sequences for homology. This will provide DArT sequences incorporation into publicly genomics resources. Attribution of putative gene functions can also be done for the non-redundant DArT marker sequences that may aid in identifying markers with putative disease resistance-related functions esp. Cassava Brown Steak Disease (CBSD) and Cassava Mosaic Disease (CMD). This will assist in employing the available data in an enhanced way.

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Reviewer #1: No

Reviewer #2: Yes: Manjusha Verma

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Genetic diversity of local and introduced cassava germplasm in Burundi using DArTseq molecular analyses

PONE-D-21-23112R1

Dear Dr. pierre,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

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Kind regards,

Amit Kumar Singh

Academic Editor

PLOS ONE