10.25338/B8K03W
Parker, Travis
0000-0002-1233-7829
University of California, Davis
Lopes de Sousa, Lorenna
0000-0002-1154-5394
University of California, Davis
de Oliveira Floriani, Talissa
0000-0003-1380-1037
University of California, Davis
Palkovic, Antonia
University of California, Davis
Gepts, Paul
0000-0002-1056-4665
University of California, Davis
Towards the introgression of PvPdh1 for increased resistance to pod
shattering in common bean
Dryad
dataset
2020
Clif Family Foundation
https://ror.org/00y0dmr19
Lundberg Family Farms*
2020-12-18T00:00:00Z
2020-12-18T00:00:00Z
en
https://doi.org/10.1007/s00122-020-03698-7
1005542 bytes
3
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Some varieties of common bean (Phaseolus vulgaris L.) suffer from pod
shattering, which can severely reduce yields, especially in arid
conditions. The PvPdh1 locus on chromosome Pv03 has recently been
described as a major locus controlling pod shattering in common bean and
could be used to mitigate pod shattering in the future. Despite this, the
role of a possible second locus on chromosome Pv08 remains unclear and
patterns of dominance and epistasis between alleles of these genes have
not been resolved. This information will be vital for efficient selection
to decrease pod shattering. Further, the genetic diversity around the
PvPdh1 gene has not yet been thoroughly explored and there are not yet
genetic screens that can be used to evaluate pod shattering in segregating
populations. Here, we have developed a recombinant inbred population to
determine the roles of genes implicated in pod shattering and evaluate the
patterns of dominance among the relevant alleles. Our results suggest that
a PvPdh1 allele reduces pod valve twisting, and its dominance varies by
phenotyping method. This allele is the only genetic variant that provides
environmentally stable and widespread resistance to pod shattering in
Middle American common beans grown for grain. Further analyses identified
a selective sweep around PvPdh1 with greater nucleotide diversity in
individuals with the ancestral, shattering-susceptible allele. Finally, we
developed simple, effective CAPS markers to facilitate the introgression
of PvPdh1 into new varieties of common bean. These genetic resources will
be critical for improving the aridity resilience of a major global staple.
Three populations were evaluated in this study; a biparental population
and two diversity panels, which represent each of the two domestication
events of common bean. The biparental population was developed to study
two shattering-related QTLs, their patterns of dominance, and their
interactions. Cultivars ‘Mayflower’ (ecogeographic race Mesoamerica, Kelly
et al. 1989) and ‘Bill Z’ (race Durango, Wood et al. 1989) showed total
resistance to pod shattering when field-grown in Davis in 2017 (n=27,
n=19, respectively). These varieties were among the most distantly related
accessions in the MDP, with neither showing any evidence of admixture
between ecogeographic races (Moghaddam et al. 2016; Parker et al. 2020).
Mayflower is a navy bean type (white, small-seeded), which possesses a SNP
allele on Pv08 that is weakly associated with resistance to pod shattering
in race Mesoamerica. Bill Z is a pinto bean type and has a SNP variant on
Pv03 associated with strong PvPdh1-mediated shattering resistance common
in race Durango. The population can therefore be used to determine if a
reduction in pod shattering was independently selected in each of these
ecogeographic races. An F3 population of 138 individuals was developed by
hybridization between these cultivars. Each F3 individual was descended
from a distinct F2 plant, and all of the F2s were the progeny of a single
F1 developed by cross-pollinating Mayflower and Bill Z. This 138-member
Mayflower x Bill Z (MxB) population was used to validate the possible
alleles on Pv03 and Pv08 and test any patterns of dominance and epistasis
between the loci. The two diversity panels were grown to evaluate the
degree of pod shattering across diverse accessions of common bean. In
2016, 98 members of major market classes in the Andean Diversity Panel
(ADP, Cichy et al. 2015) were field-grown in Davis, California, to
evaluate each variety’s susceptibility to pod shattering. In 2017, 278
varieties of the BeanCAP Middle American Diversity Panel (MDP, Moghaddam
et al. 2016) were similarly field-grown in Davis to evaluate pod
shattering. At maturity, a sample of pods (mean n = 30) was harvested from
each variety. Mature pods of all phenotyped varieties were harvested and
then exposed to seven days of desiccation at 65°C and a further seven days
of re-equilibration to room temperature. The desiccation conditions for
all varieties were identical and desiccation was conducted using the same
drying chamber. The proportion of pods dehiscing in this treatment was
recorded, along with the market class of each variety. For evaluation of
pod twists in the MxB population, all non-shattering pods were fractured
by hand and then all pods were subjected to the desiccation treatment and
re-equilibration again. The number of twists was counted for ten pods of
each genotype, with “1” indicating a complete 360° rotation of the valve.
DNA was extracted from young trifoliate leaves (approximately 1cm in
length) of the greenhouse-grown biparental MxB F3 generation, using a
modified CTAB protocol (adapted from Allen et al. 2006). DNA was
quantified with a NanoDrop spectrophotometer and genotyped using the
BARCBean6K_3 BeadChip (Song et al. 2015), yielding 5398 initial SNPs. SNPs
that were missing or heterozygous in either parent, or identical between
the parents, were filtered from further analysis. The remaining SNPs were
arranged into a linkage map using the ASMap R package (Taylor et al.
2017). SNPs that did not map to one of the 11 major linkage groups were
removed, leaving 1794 SNPs for QTL mapping. QTL mapping was conducted
using the expectation maximization method (Lander and Botstein 1989) in
R/qtl (Broman et al. 2003). Phenotypes for QTL mapping were generated by
harvesting all the pods from each greenhouse-grown F3 plant (mean n=27
pods/plant), then subjecting them to seven days at 65°C and seven further
days of re-equilibration to room temperature. Pods that had fractured to
the tip of the beak due to this treatment were counted as shattered, while
those with no opening or only fissuring along the sutures were considered
non-shattering. The percentage of pods that shattered in this treatment
were used for QTL mapping. The maximum LOD score of 1000 randomized
analyses of the data was used as a significance threshold. To test
dominance, F3 individuals were subset by genotype at highly significant
SNPs, and comparisons were made between groups by t-test. Next, the 43
SNPs within 100kb of PvPdh1 in the MDP data set were analyzed to identify
patterns of selection and diversity around the gene. To simplify and
visualize the data, principal component analysis was performed on the SNPs
using R. Sequence variation was converted to integer values and the
imputePCA() function of the missMDA package was used to impute missing
data (Josse and Husson 2016). The genotype data were also sorted to
identify unique haplotypes within the populations. The degree of
similarity between the PCA and haplotype diversity was then compared.
Individuals with missing data for SNPs distinguishing the haplotypes or
haplotype clusters were not shown in plots, and not numbered in plots as
they could not be unambiguously placed within any haplotype group. The
SNPs tightly linked to PvPdh1 in the MDP data set were then screened for
other positions that could be useful for conversion to additional CAPS
markers. The SNP closest to PvPdh1 in this data set, at Pv03 position
49,132,438 (accession G19833 genome v2.1), is distinguishable by EcoRI and
is highly correlated with pod shattering. Unlike the TaqII-based CAPS
marker, the allele cleaved by EcoRI is the shattering-resistant variant,
reducing the risk of falsely identifying a susceptible individual as
resistant due to technical errors in digestion. The SNP distinguished by
EcoRI is separated from the PvPdh1 causal polymorphism by less than 7kb.