Morphological and Agronomic Characterization of Spanish Landraces of Phaseolus vulgaris L.
and Monica Boscaiu 4,*Round 1
Reviewer 1 Report
Review of Agriculture
Morphological and Agronomic Characterization of Spanish Landraces of Phaseolus vulgaris L.
Sugenith Arteaga, Lourdes Yabor, José Torres, Eva Solbes, Enrique Muñoz, María José Díez, Oscar Vicente and Monica Boscaiu
The authors provide a very detailed description of 45 agronomic characters of 24 Spanish landraces of common bean (Phaseolus vulgaris). They examined 17 quantitative and 28 qualitative traits during the autumn and then the subsequent spring of 5 individuals from each of these 24 landraces. They then performed principal components analyses of their data, and showed that many of the examined traits showed high variability between the landraces. They also found that many of the landraces exhibited differences between these traits when grown in the autumn and in the spring, showing that these traits were strongly influenced by the environment.
Overall, this is an impressive compilation of data, that should be useful to bean breeders. One major concern I have is that only 5 plants were examined for each landrace during each growing season. Since many of the traits examined showed very high standard deviations and coefficients of variance, this raises the question whether 5 samples are sufficient to draw significant conclusions. As the authors note in their discussion, they observed remarkably high coefficients of variation for many of the traits they studied. They present this in the context of showing that these landraces are potentially a good source of genetic diversity, but I worry that his might also reflect the small sample size for each land-race.
A second concern I have is how these values compare with commercial varieties. For example, are the yields similar to commercial varieties, or so low that growers are unlikely to adopt them or even attempt to cross them in for fear of contaminating their germplasm?
A third concern I have is how might this data be used? Characters such as yield and plant height clearly affect agronomic performance. In contrast, what agronomic importance is there to characters such as hypocotyl length, leaf shape or flower color? The authors should point out the significance of these characters to non-bean specialists, especially since they state in their discussion that their work might help in breeding cultivars better suited to the more extreme climates we are likely to experience in the coming years. Please provide more guidance on which of these traits might be useful, and why? For example, I can see why different leaf shapes might affect tolerance to high temperature and drought since this will affect transpiration and heat dissipation. In contrast, what difference does flower shape or color make, and what should breeders be looking for in order to improve yield or tolerance to unfavorable environments? Similarly what difference does hypocotyl color make? This isn’t being picky: perhaps the authors might have identified biomarkers for plant improvement. For example, if hypocotyl length or color is positively-correlated with desirable outcomes as adults, then screening for longer, or shorter, hypocotyls or for hypocotyls of a desired color can be performed at a much earlier stage in the growth cycle. I would therefore like to see the authors spend more time discussing how their analysis might be used to improve P. vulgaris, especially its tolerance to climate change and the associated drought stress. Which traits showed the most promise, and why? Did you identify any promising landraces to incorporate into breeding programs, or any duds to avoid?
However, my most serious concern is just how much does this study add to information about Spanish bean land-races? For example, Rodiño et al (2003) Euphytica 131, 165−175 examined 47 characters of 388 Spanish bean landraces, while Escribano et al (1998) Plant Breed. 117, 49-56 studied 66 landraces and Gil and De Ron (1992) Plant Breed. 109, 313−319 studied 51 accessions. Thus, assuming there is no overlap in landraces between these reports, this study is increasing the pool of described land-races by less than 5%. What new and different information does this study provide? Do they identify any trends missed by the earlier studies, or any great candidates for bean improvement?
Overall the English was understandable, but there were many mistakes and awkward phrasings. I flag a few below, but there are many more which I do not have time to flag or correct.
Line 18 should be “…originates from a Mesoamerican and from an Andean gene pool… “
Line 24: it seems unlikely that most readers will be familiar with ‘IBPGR descriptors,’ so this acronym should be spelled out and a succinct explanation of these descriptors should be provided.
Lines 38-39: please acknowledge that this hypothesis is not universally accepted and that some evidence shows that the Andean gene pool is derived from Mesoamerican progenitors.
Line 51 “orchards” is a term used for cultivated fruit trees. Do the authors mean to say “farms” or “fields?”
Line 53 should be “…stocks, resulting in new genetically intermediate forms…”
Line 106: is it 5 individuals per plot, or 5 individuals per pot? If each plot contained 5 individual plants in separate pots, how were these plots arranged given that some plants grew much taller than others and might therefore shade their shorter neighbors.
Line 120: Please reformat this table and all others so that all columns are aligned to the left side of the column. The present format is difficult to read.
Line 125 and throughout the paper: Please change “interaction genotype x environment” to “interaction between genotype and the environment”
Lines 167-168 are hard to understand. Please rewrite for clarity,
Line 199: should “per-shaped” be “pear-shaped?”
Table 4 formatting must be corrected since the header line is duplicated in the middle of the table, which throws the subsequent rows out of register.
Page and line numbering is reset to 1 after table
Author Response
We would like to thank the three reviewers for their comments, which have helped us to improve the quality of the manuscript. Following their suggestions, we have prepared a revised version of the manuscript, which we believe gives satisfactory answers to all questions included in their reports on the original version.
In the next paragraphs, we provide detailed and point-by-point answers to the specific questions and concerns raised by each of the three reviewers.
The authors provide a very detailed description of 45 agronomic characters of 24 Spanish landraces of common bean (Phaseolus vulgaris). They examined 17 quantitative and 28 qualitative traits during the autumn and then the subsequent spring of 5 individuals from each of these 24 landraces. They then performed principal components analyses of their data, and showed that many of the examined traits showed high variability between the landraces. They also found that many of the landraces exhibited differences between these traits when grown in the autumn and in the spring, showing that these traits were strongly influenced by the environment.
Overall, this is an impressive compilation of data, that should be useful to bean breeders. One major concern I have is that only 5 plants were examined for each landrace during each growing season. Since many of the traits examined showed very high standard deviations and coefficients of variance, this raises the question whether 5 samples are sufficient to draw significant conclusions. As the authors note in their discussion, they observed remarkably high coefficients of variation for many of the traits they studied. They present this in the context of showing that these landraces are potentially a good source of genetic diversity, but I worry that his might also reflect the small sample size for each land-race.
· Answer: We agree that 5 plants can be considered as insufficient for drawing significant conclusions, even though this number of has been used in many similar studies on the phenotypic characterisation of crops (such as, Valcarcel JV et al. Morphological characterization of the cucumber (Cucumis sativus L.) collection of the COMAV’s Genebank, Genetic Resources and Crop Evolution 2018; Carvalho Santos R et al. Morphological characterization of leaf, flower, fruit and seed traits among Brazilian Theobroma L. species, Resources and Crop Evolution 2012). However, although the number of plants from each accession was five in each cycle, the number of observations (whenever possible) was much higher. All pod and seed traits analyses were based on a considerably higher number of measurements, as we analysed five pods and ten seeds per plant. We apologise for not explaining this properly in ‘Material and methods’ of the original version of the manuscript. In the new version, we added an explanatory sentence in section 2.2
A second concern I have is how these values compare with commercial varieties. For example, are the yields similar to commercial varieties, or so low that growers are unlikely to adopt them or even attempt to cross them in for fear of contaminating their germplasm?
Answer: Compared with commercial varieties, the traditional ones can be less productive, in a general sense. However, the cultivation of traditional varieties, although replaced in many cases by the commercial ones, is still done by local farmers. Some of the reasons are their higher quality and the adaptation to the specific agroclimatic conditions in which this traditional variety has been cultivated for decades o even centuries. Also, in some cases, the specific organoleptic characteristics of a given variety makes it unique for the preparation of specific traditional culinary dishes in the area of cultivation. The substitution of the traditional variety for a commercial one changes the sensory quality of the traditional meal, losing its value. Thus, to our understanding, the cultivation of traditional varieties is not only a matter of yield, as it involves a much more complex scenario, including important cultural aspects.
A third concern I have is how might this data be used? Characters such as yield and plant height clearly affect agronomic performance. In contrast, what agronomic importance is there to characters such as hypocotyl length, leaf shape or flower color? The authors should point out the significance of these characters to non-bean specialists, especially since they state in their discussion that their work might help in breeding cultivars better suited to the more extreme climates we are likely to experience in the coming years. Please provide more guidance on which of these traits might be useful, and why? For example, I can see why different leaf shapes might affect tolerance to high temperature and drought since this will affect transpiration and heat dissipation. In contrast, what difference does flower shape or color make, and what should breeders be looking for in order to improve yield or tolerance to unfavorable environments? Similarly what difference does hypocotyl color make? This isn’t being picky: perhaps the authors might have identified biomarkers for plant improvement. For example, if hypocotyl length or color is positively-correlated with desirable outcomes as adults, then screening for longer, or shorter, hypocotyls or for hypocotyls of a desired color can be performed at a much earlier stage in the growth cycle. I would therefore like to see the authors spend more time discussing how their analysis might be used to improve P. vulgaris, especially its tolerance to climate change and the associated drought stress. Which traits showed the most promise, and why? Did you identify any promising landraces to incorporate into breeding programs, or any duds to avoid?
Answer: Following the comments of the reviewer, we have skipped some of the evaluated traits. Although all the descriptors used are included in the IPGRI list and are widely used by breeders and in research on plant genetic resources, we understand that some of them (although interesting for other purposes, such as variety registration of for botanical studies) are not directly related to the objective of this work. Therefore, we have deleted all data on the following traits: Hypocotyl pigmentation, Emerging cotyledon color, Leaf color of chlorophyll, Leaf persistence when 90% of pods in the plot are dry, Color of standards, Color of wings, Flower bud size, Size of bracteole, Bracteole/Calyx length relation and Wing opening.
Regarding your comment: “I would therefore like to see the authors spend more time discussing how their analysis might be used to improve P. vulgaris, especially its tolerance to climate change and the associated drought stress”, the major aim of this manuscript is to give information about the morpho-agronomic characteristics of this specific set of accessions, which has also been evaluated for tolerance to abiotic stresses. In a new manuscript (in preparation) we will discuss what accessions are the most promising in terms of their stress tolerance, and breeders will find the morpho-agronomic characteristics of these accessions in the present publication.
However, my most serious concern is just how much does this study add to information about Spanish bean land-races? For example, Rodiño et al (2003) Euphytica 131, 165−175 examined 47 characters of 388 Spanish bean landraces, while Escribano et al (1998) Plant Breed. 117, 49-56 studied 66 landraces and Gil and De Ron (1992) Plant Breed. 109, 313−319 studied 51 accessions. Thus, assuming there is no overlap in landraces between these reports, this study is increasing the pool of described land-races by less than 5%. What new and different information does this study provide? Do they identify any trends missed by the earlier studies, or any great candidates for bean improvement?
Answer: The landraces selected for the present work were not included in the papers cited by the reviewer. As mentioned above, the accessions included in this work have also been tested for their tolerance to abiotic stresses, and the results are being analysed at present (manuscript in preparation). The information provided by the two complementary publications (if finally accepted) will be of great value for breeders, when selecting some accessions to be used in breeding programmes. We considered that it was not possible to publish the large amount of data regarding both, phenotypic characterisation and tolerance to abiotic stresses, in a single paper, and decidedto split all the available data in two manuscripts. The reviewer’s comment is correct, when considering only this manuscript, as the interest of this particular set of bean accessions depends on the characterisation of their responses to drought and salinity, which will be reported independently (hopefully) in the second publication.
Overall the English was understandable, but there were many mistakes and awkward phrasings. I flag a few below, but there are many more which I do not have time to flag or correct.
Answer: The English grammar and style of the manuscript has been thoroughly revised and corrected. All specific changes suggested by the reviewer – regarding grammar mistakes, typos, word use, format issues, etc. – have been introduced in the revised version of the manuscript as indicated, and are not mentioned individually here.
Line 24: it seems unlikely that most readers will be familiar with ‘IBPGR descriptors,’ so this acronym should be spelled out and a succinct explanation of these descriptors should be provided.
Answer: ‘IBPRG’ is spelt-out in the Abstract, and its meaning has been briefly explained in the text (section 2.2. Descriptors Used for the Agronomic Characterization)
Lines 38-39: please acknowledge that this hypothesis is not universally accepted and that some evidence shows that the Andean gene pool is derived from Mesoamerican progenitors.
Answer: This section has been modified to clarify the existing gene pools of Phaeolus
Line 106: is it 5 individuals per plot, or 5 individuals per pot? If each plot contained 5 individual plants in separate pots, how were these plots arranged given that some plants grew much taller than others and might therefore shade their shorter neighbors.
Answer: It is 5 plants (and pots) per plot, as each plant was grown in an individual pot, organized on a line with sufficient distance between them
Lines 167-168 are hard to understand. Please rewrite for clarity,
Answer: Done
Reviewer 2 Report
The manuscript has been well written and presented. Conceptualization, data and conclusion are convincing. Although, authors need to do following minor changes before it goes for publication:
1. Abstract is good but authors needs to do a separation while stating data in terms of morphological and agronomic traits.
2. Introduction sentences from line 59 to 64 where authors are talking about world production should come earlier in the section. Also, from line 79 to forthcoming are again stated discussing about yield which again shows a disconnect in thoughts. Overall, introduction material is good but must be rearranged.
3. There is no scale bar in seed pictures in figure 1? Some seeds look smaller. Are they smaller or it is happening due to compression of original picture? Although, figure one is good. Though, figure 3 has the scale bar. But it will look good if figure 1 may also be added with scale bar.
4. Figure 2 data is not visible.
5. Table 1 is messed up. Authors may align the contents or present in landscape format to accommodate this huge information.
6. Figure 5 scatter plot: Please stretch more this figure to look how we can see more separation and the data may look better.
7. Figure 8 and 9: Graph colors are not very visible.
Author Response
We would like to thank the three reviewers for their comments, which have helped us to improve the quality of the manuscript. Following their suggestions, we have prepared a revised version of the manuscript, which we believe gives satisfactory answers to all questions included in their reports on the original version.
In the next paragraphs, we provide detailed and point-by-point answers to the specific questions and concerns raised by each of the three reviewers.
The manuscript has been well written and presented. Conceptualization, data and conclusion are convincing. Although, authors need to do following minor changes before it goes for publication:
Abstract is good but authors needs to do a separation while stating data in terms of morphological and agronomic traits.
Answer: The Abstract has been accordingly modified
Introduction sentences from line 59 to 64 where authors are talking about world production should come earlier in the section. Also, from line 79 to forthcoming are again stated discussing about yield which again shows a disconnect in thoughts. Overall, introduction material is good but must be rearranged.
Answer: The text in the Introduction has been rearranged, following the reviewer’s suggestion
There is no scale bar in seed pictures in figure 1? Some seeds look smaller. Are they smaller or it is happening due to compression of original picture? Although, figure one is good. Though, figure 3 has the scale bar. But it will look good if figure 1 may also be added with scale bar.
Answer: Fig. 1 is meant to show the geographical origin of the seeds, not their relative size (which is shown in Fig. 3); therefore, no scale bars were included in Fig. 1
Figure 2 data is not visible.
Answer: Figure 2 has been replaced by a new one with better contrast and more resolution
Table 1 is messed up. Authors may align the contents or present in landscape format to accommodate this huge information.
Answer: The table has been reorganised and extensively modified (following also the suggestion of reviewer 1)
Figure 5 scatter plot: Please stretch more this figure to look how we can see more separation and the data may look better.
Answer: Done
Figure 8 and 9: Graph colors are not very visible.
Answer: The figures have been modified, following the reviewer’s comment
Reviewer 3 Report
The manuscript untitled “Morphological and Agronomic Characterization of
Spanish Landraces of Phaseolus vulgaris L.” by Arteaga et al addresses the morphological and agronomic traits charcaterization in 24 local landraces of common bean from Spain. This paper is of major importance as several landraces are key genetic resources for the breeders to cope with abiotic stresses. Overall, the manuscript is well organized and reuslts are very promissing, and porvide importante insights on local landraces characterization with high potential for supplementing one of the common bean gene pools.
However, the manuscript need to be edited for the english language, wih several typos are rephrasing needed.
In the Introduction section, i would advice to clarify L37-L39, in order to understand that the common bean has two centres of in the American continent: the Middle American and the Andean centres.
After, i would recommend the rewritng of the section L41-L58, to accomadate the following information: first, the determination of the two gene pools of common bean and only after, the focus and imporance of Mesoamerican gene pool in comparision with South Andean gene pool. Also, it would be advantageous to follow the gene pool classification by https://www.cwrdiversity.org/CWR-Checklist/pages/genepool-details/genepool-details.php?id%5B%5D=16&id%5B%5D=383&.
L65- “Much of the genetic variability of this crop has been collected and conserved in germplasm banks.”- please rephrase, as the genetic diversity is not collected is characterized, what is collected are seeds that are conserved ex situ in germplasm banques and their genetic diversity characterized, as well as morphological traits.
On Results sections, I would recommend to perform a matrix of distances with the traits gather and do a UPGMA that will enrich the results and as thhe discussion, besides the descriptive statistics and PCA analysis. This will allow to access clustering of landraces that would benefit the discussions accordingly.
Also, Discussion need be improved to accomodate the new analysis and to provide clear indications of the potential of the local landraces screened within MesoAmerican Gene pool, as Peninsula Iberia a secondary center of diversification.
Author Response
We would like to thank the three reviewers for their comments, which have helped us to improve the quality of the manuscript. Following their suggestions, we have prepared a revised version of the manuscript, which we believe gives satisfactory answers to all questions included in their reports on the original version.
In the next paragraphs, we provide detailed and point-by-point answers to the specific questions and concerns raised by each of the three reviewers.
The manuscript untitled “Morphological and Agronomic Characterization of Spanish Landraces of Phaseolus vulgaris L.” by Arteaga et al addresses the morphological and agronomic traits charcaterization in 24 local landraces of common bean from Spain. This paper is of major importance as several landraces are key genetic resources for the breeders to cope with abiotic stresses. Overall, the manuscript is well organized and reuslts are very promissing, and porvide importante insights on local landraces characterization with high potential for supplementing one of the common bean gene pools.
However, the manuscript need to be edited for the english language, wih several typos are rephrasing needed.
Answer: English grammar and style have been revised
i would advice to clarify L37-L39, in order to understand that the common bean has two centres of in the American continent: the Middle American and the Andean centres.
After, i would recommend the rewritng of the section L41-L58, to accomadate the following information: first, the determination of the two gene pools of common bean and only after, the focus and imporance of Mesoamerican gene pool in comparision with South Andean gene pool. Also, it would be advantageous to follow the gene pool classification by https://www.cwrdiversity.org/CWR-Checklist/pages/genepool-details/genepool-details.php?id%5B%5D=16&id%5B%5D=383&.
Answer: The paragraphs have been modified according to the reviewer’s suggestion. One reference has been added (Bitocchi et al., 2012) to clarify the importance of the Mesoamerican gene pool in comparison with the Andean one.
L65- “Much of the genetic variability of this crop has been collected and conserved in germplasm banks.”- please rephrase, as the genetic diversity is not collected is characterized, what is collected are seeds that are conserved ex situ in germplasm banques and their genetic diversity characterized, as well as morphological traits.
Answer: The sentence has been rephrased according to the reviewer’s suggestion.
On Results sections, I would recommend to perform a matrix of distances with the traits gather and do a UPGMA that will enrich the results and as thhe discussion, besides the descriptive statistics and PCA analysis. This will allow to access clustering of landraces that would benefit the discussions accordingly.
Also, Discussion need be improved to accomodate the new analysis and to provide clear indications of the potential of the local landraces screened within MesoAmerican Gene pool, as Peninsula Iberia a secondary center of diversification.
Answer: The matrix of distances has been calculated and has been used to do a tree using the UPGMA grouping method. The clustering of landraces has been included in a new figure and the results are presented in the Result section and discussed in the Discussion section.
Round 2
Reviewer 1 Report
The authors have corrected the issues raised in my previous review, so I'm ready to approve publication.
Reviewer 3 Report
The authors have done a significant improvement of the manuscript, which is very interesting with the incorporation of UPGMA and PCA analysis.
