Genetic and Genomic Diversity in a Tarwi (Lupinus mutabilis Sweet) Germplasm Collection and Adaptability to Mediterranean Climate Conditions
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Materials
2.2. Morphological Analysis
2.3. Molecular Analysis
2.4. Flow Cytometry
3. Results
3.1. Morphological Characterization and Genetic Parameters among Accessions
3.2. Diversity Assessed by Molecular Markers
3.3. Diversity Assessed by Genomic Traits
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Acronym | Trait 1 | Method (unit) |
---|---|---|
DUF | Days from sowing until flowering 3 | Counting (nr 4) |
NLMS | Number of leaves on the main stem | Counting (nr) |
HUFF | Height up to first flower | Metric meas. 5 (cm) |
ADNL | Average distance between leaves | = HUFF/NLMS (cm) |
NPMS | Number of pods on the main stem | Counting |
PLMS | Pod length on the main stem | Metric meas. (cm) |
PWMS | Pod width on the main stem | Metric meas. (cm) |
RBLWPMS | Ratio length-width of pods on the main stem | = PLMS/PWMS (dim. 6) |
NSMS | Number of seeds on the main stem | Counting (nr) |
SLMS | Seed length on the main stem 2 | Metric meas. (cm) |
SWMS | Seed width on the main stem | Metric meas. (cm) |
RBLWSMS | Ratio length-width of seed on the main stem 2,3 | = SLMS/SWMS (dim.) |
NSPMS | Number of seed per pod on the main stem | Counting (nr) |
WSMS | Weight of seeds on the main stem | Weighting (g) |
TSWMS | Thousand seeds weight on the main stem 2 | = WSMS/NSMS*1000 (g) |
NPB | Number of primary branches | Counting (nr) |
ADBPB | Average distance between primary branches 2,3 | = HUFF/NPB (cm) |
SLPB | Sum of the length of primary branches | Metric meas. (cm) |
ALPB | Average length of primary branches | = SLPB/NPB (cm) |
PBL | Proportion of leaves with branches 2,3 | = NPB/NLMS (%) |
NPPB | Number of pods on primary branches 2 | Counting (nr) |
NSPB | Number of seeds on primary branches 2 | Counting (nr) |
NSPPB | Number of seeds per pod on primary branches | = NSPB/NPPB (nr) |
NPPPB | Number of pods per primary branch | = NPPB/NPB (nr) |
WSPB | Weight of seeds on primary branches 2 | Weighting (g) |
WSPPB | Thousand seeds weight per primary branches | Weighting (g) |
TSWPB | Thousand seeds weight on primary branches | = WSPB/NSPB × 1000 (g) |
TBL | Total branch length | = SLPB+ HUFF |
TNP | Total number of pods 2 | Counting (nr) |
TNS | Total number of seeds | Counting (nr) |
TNSPP | Total number of seeds per pod | = TNS/TNP (nr) |
TW | Total seed weight | Weighing (g) |
PSMS | Percentage of seed weight on the main stem | = WSMS/TW (%) |
PSPB | Percentage of seed weight on primary branches 3 | = WSPB/TW (%) |
TTSW | Total thousand seeds weight | = TW/TNS × 1000 (g) |
SWBLR | Seed weight/total branch length ratio | = TW/TBL × 100 (g/m) |
Accession | SFC 2 | DUF 3 | NLMS | HUFF | NPB | SLPB | PBL | TBL |
---|---|---|---|---|---|---|---|---|
JKI-L309 | D | 80.8 a | 12.9 a | 40.0 a | 2.8 abc | 81.9 a | 21.6 efgh | 122.0 a |
JKI-L377 | B | 92.8 b | 12.8 a | 47.7 bc | 2.7 ab | 87.2 a | 19.9 cde | 137.7 ab |
MUTAL | A | 93.5 b | 14.8 b | 60.0 gh | 3.3 efg | 152.0 h | 22.8 efgh | 213.1 i |
JKI-L210 | C | 96.4 c | 15.8 def | 50.0 bcd | 3.0 cde | 89.1 a | 19.1 bc | 142.2 bc |
LM13 | C | 97.7 cd | 16.5 fg | 53.0 cdef | 3.9 ijk | 132.0 cdefg | 23.3 efghi | 185.6 efgh |
LM81 | C | 97.8 cd | 15.2 bcd | 54.3 cdef | 3.3 cdef | 127.0 bcdef | 21.7 defgh | 182.4 defgh |
JKI-L295 | A | 98.6 cd | 16.2 f | 60.7 fgh | 2.6 a | 114.1 b | 16.3 a | 175.2 def |
LM268 | A | 98.8 cd | 16.3 f | 60.9 gh | 3.6 hij | 133.3 defgh | 22.2 efgh | 194.2 fghi |
PRT79 | C | 98.8 cd | 17.4 hi | 65.1 hi | 3.5 hij | 136.2 efgh | 20.4 cde | 202.3 ghi |
I82 | D | 99.9 cd | 15.9 def | 52.4 cde | 3.4 fghi | 115.8 bc | 21.2 def | 169.0 de |
LM34 | D | 100.1 cd | 15.2 bcd | 50.9 bcd | 3.7 hijk | 124.5 bcde | 24.3 i | 175.6 de |
Potosi-ALE | C | 100.3 cd | 15.0 b | 53.6 cde | 3.5 fghi | 134.2 bcdef | 23.4 fghi | 188.7 efgh |
LM27 | A | 100.4 cd | 15.9 cdef | 55.8 efgh | 3.5 fghi | 125.3 bcdef | 21.9 defgh | 181.7 efgh |
Potosi-ISA | C | 100.5 cd | 16.7 fg | 58.9 efgh | 3.4 fghi | 118.5 bcd | 20.7 cde | 177.5 def |
LM18 | C | 100.5 cd | 17.7 ghi | 54.6 defg | 3.7 hij | 127.8 bcdef | 20.8 cde | 182.5 defg |
CM157 | C | 100.6 cd | 15.4 bcde | 49.1 bcd | 3.0 bcd | 111.4 b | 18.6 bc | 160.7 cd |
XM-5 | B | 101.2 cd | 16.4 fg | 58.5 efgh | 3.5 fghi | 125.0 bcdef | 21.3 defg | 184.1 efgh |
LM32 | C | 101.6 d | 16.2 ef | 53.7 cdef | 3.4 fgh | 125.3 bcdef | 21.5 def | 179.6 defg |
LM231 | C | 102.4 d | 18.0 i | 64.8 hi | 4.6 k | 163.2 gh | 25.5 ghi | 229.4 hi |
P20993 | B | 102.6 d | 15.1 bc | 55.3 defg | 3.6 ghij | 125.1 bcdef | 23.5 hi | 180.4 defg |
INTI | C | 102.6 cd | 17.7 i | 68.9 i | 3.3 def | 147.0 fgh | 18.6 b | 218.7 i |
SBP | C | 103.0 d | 16.0 f | 58.6 efgh | 3.2 def | 119.7 bcdef | 19.7 bcd | 179.4 defgh |
XM1-39 | C | 103.4 d | 16.2 f | 54.6 defg | 3.1 def | 110.3 bc | 18.7 bc | 166.4 de |
Mihai | 97.6 cd | 16.6 fgh | 42.6 ab | 3.7 hijk | 122.1 bcdef | 22.5 defgh | 164.7 cde | |
Misak | 98.6 cd | 18.8 j | 38.2 a | 3.8 jk | 120.7 bcdefg | 20.4 cde | 158.9 cd | |
p-value 4 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | |
p-value 5 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.020 | 0.000 | |
p-value 6 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
Accession | TNP 2 | TNS | TNSPP | TTSW | PSMS | PSPB | TW | SWBLR |
---|---|---|---|---|---|---|---|---|
JKI-L210 | 11.5 a | 36.6 ab | 3.3 fg | 101.4 a | 87.8 | 12.2 | 3.7 a | 1.3 a |
INTI | 13.7 a | 37.4 ab | 2.7 bcd | 154.0 cd | 74.6 | 25.4 | 5.7 b | 2.3 ef |
XM1-39 | 13.9 ab | 36.1 ab | 2.8 bcd | 180.4 jkl | 78.1 | 21.9 | 6.3 b | 1.3 a |
JKI-L377 | 19.8 cdef | 61.3 cde | 3.0 ef | 103.7 a | 72.2 | 27.8 | 6.3 b | 3 def |
JKI-L309 | 16.1 bc | 49.2 cd | 3.1 efg | 159.7 ef | 72.2 | 27.8 | 7.8 c | 3.1 fg |
SBP | 16.8 cd | 43.6 bc | 2.6 bc | 188.7 lm | 77.0 | 23.0 | 8.0 cd | 1.7 abc |
LM32 | 22.1 efg | 56.7 def | 2.7 bcd | 150.8 cde | 67.3 | 32.7 | 8.4 cde | 1.1 ab |
Potosi-ALE | 25.0 gh | 62.2 efg | 2.6 b | 182.7 bc | 59.1 | 40.9 | 8.4 cdef | 1.5 abcd |
LM34 | 24.9 gh | 67.9 fg | 2.7 bcde | 131.6 b | 55.0 | 45.0 | 8.5 cde | 1.6 abcd |
JKI-L295 | 18.0 cde | 48.0 cd | 2.7 bcd | 188.4 m | 80.3 | 19.7 | 9.0 def | 2.2 bcdef |
LM231 | 22.9 fgh | 59.9 def | 2.6 bcd | 169.4 fgh | 56.2 | 43.8 | 9.5 cdef | 1.5 abcd |
MUTAL | 19.2 def | 52.2 cd | 2.8 bcd | 184.7 lm | 67.2 | 32.8 | 9.6 def | 3.3 g |
LM81 | 23.1 gh | 63.1 fg | 2.9 bcde | 157.8 ef | 57.7 | 42.3 | 9.7 fghi | 1.8 abcde |
LM13 | 22 fgh | 57.5 def | 2.7 bcd | 179.0 ijk | 70.3 | 29.7 | 9.9 efgh | 1.8 abcde |
XM-5 | 23.8 gh | 59.7 def | 2.6 bc | 170.1 ghi | 61.2 | 38.8 | 9.9 defg | 1.9 abcde |
CM157 | 23.0 gh | 64.9 efg | 2.8 cde | 157.3 def | 61.6 | 38.4 | 10.0 fghij | 2.1 abcdef |
LM27 | 23.0 efg | 62.0 def | 2.8 bcde | 178.4 ghijk | 64.1 | 35.9 | 10.5 fghij | 1.8 abcde |
PRT79 | 22.5 gh | 62.8 fg | 2.8 de | 177.6 hijk | 58.3 | 41.7 | 11.1 ghijk | 2.1 abcde |
P20993 | 24.8 hi | 67.7 g | 2.8 bcde | 168.9 fg | 58.0 | 42.0 | 11.1 ijk | 2.1 abcdef |
I82 | 21.8 efg | 64.5 fg | 3.1 efg | 175.4 ghij | 62.5 | 37.5 | 11.2 ghijk | 2.2 def |
Potosi-ISA | 23.7 gh | 64.3 fg | 3.1 bcde | 184.0 klm | 55.7 | 44.3 | 11.5 jk | 2.3 bcdef |
LM18 | 23.2 gh | 66.1 efg | 2.9 def | 190.5 lm | 52.1 | 47.9 | 12.6 hijk | 2.2 cdef |
LM268 | 22.1 gh | 50.5 cd | 2.2 a | 289.2 n | 40.9 | 59.1 | 13.8 k | 2.7 abcdef |
Mihai | 25.7 hi | 101.2 h | 4.0 h | 370.7 n | 28.8 | 71.1 | 36.7 l | 23.3 abcde |
Misak | 28.8 i | 98.0 h | 3.4 g | 381.5 n | 45.0 | 54.9 | 37.2 l | 22.9 abcde |
p-value 3 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
p-value 4 | 0.040 | 0.000 | 0.000 | 0.000 | 0.969 | 0.756 | 0.004 | 0.000 |
p-value 5 | 0.000 | 0.000 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
Traits | Average | Phenotypic Variance | Genotypic Variance | PCV 1 | GCV 2 | H 2,3 | ||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
2016/17 | 2017/18 | 2016/17 | 2017/18 | 2016/17 | 2017/18 | 2016/17 | 2017/18 | 2016/17 | 2017/18 | 2016/17 | 2017/18 | |
TSWMS | 184.15 | 10.94 | 1368.99 | 1779.1 | 1368.82 | 1599.4 | 20.09 | 21.91 | 20.09 | 20.77 | 1 | 0.9 |
TSWPB | 156 | 3.04 | 1423.64 | 1562.07 | 1423.39 | 1466.89 | 24.19 | 24.64 | 24.18 | 23.88 | 1 | 0.94 |
TTSW | 158.29 | 177.98 | 1145.83 | 1561.49 | 1113.07 | 1339.14 | 21.39 | 22.20 | 21.08 | 20.56 | 0.97 | 0.86 |
DUF | 87.67 | 3.04 | 17.21 | 23.25 | 16.59 | 10.85 | 4.73 | 4.52 | 4.65 | 3.09 | 0.96 | 0.47 |
WSPPB | 52.29 | 23.32 | 148.79 | 382.43 | 140.77 | 289.57 | 23.33 | 30.14 | 22.69 | 26.22 | 0.95 | 0.76 |
HUFF | 73.1 | 31.24 | 83.85 | 26.45 | 78.7 | 23.64 | 12.53 | 12.29 | 12.14 | 11.61 | 0.94 | 0.89 |
NLMS | 15.21 | 23.32 | 2.14 | 1.36 | 2 | 1.22 | 9.62 | 7.09 | 9.29 | 6.73 | 0.93 | 0.9 |
SLMS | 0.95 | 51.2 | 0 | 0.6 | 0 | 0.57 | 6.72 | 8.19 | 6.48 | 7.97 | 0.93 | 0.95 |
PWMS | 1.57 | 7.57 | 0.01 | 0.01 | 0.01 | 0.01 | 7.12 | 8 | 6.75 | 7.83 | 0.9 | 0.96 |
SWBLR | 4.31 | 192.52 | 1.31 | 0 | 1.17 | 0 | 26.54 | 20.07 | 25.09 | 18.33 | 0.89 | 0.83 |
TBL | 220.4 | 352.93 | 1183.56 | 421 | 1044.3 | 344.87 | 15.61 | 14.55 | 14.66 | 13.17 | 0.88 | 0.82 |
ALPB | 46.86 | 10.94 | 17.46 | 27.53 | 15.11 | 22.04 | 8.92 | 14.9 | 8.29 | 13.33 | 0.87 | 0.8 |
TW | 9.49 | 31.24 | 7.7 | 6391.49 | 6.73 | 6049.35 | 29.24 | 22.65 | 27.33 | 22.04 | 0.87 | 0.95 |
ADNL | 4.84 | 10.48 | 0.16 | 0 | 0.14 | 0 | 8.35 | 9.57 | 7.72 | 8.82 | 0.85 | 0.85 |
PSMS | 0.66 | 99 | 0.01 | 0.02 | 0.01 | 0.01 | 16.93 | 19.84 | 15.5 | 17.91 | 0.84 | 0.81 |
PSPB | 0.34 | 0.07 | 0.01 | 0.01 | 0.01 | 0.01 | 32.29 | 26.56 | 29.56 | 21.14 | 0.84 | 0.63 |
SLPB | 147.29 | 2.64 | 796.89 | 291.04 | 671.56 | 218.18 | 19.17 | 17.23 | 17.59 | 14.92 | 0.84 | 0.75 |
NSMS | 31.29 | 0.66 | 48.96 | 38.56 | 40.63 | 25.37 | 22.36 | 19.88 | 20.37 | 16.12 | 0.83 | 0.66 |
WSMS | 5.69 | 5.54 | 1.82 | 2.76 | 1.52 | 2.3 | 23.74 | 29.96 | 21.66 | 27.39 | 0.83 | 0.84 |
WSPB | 4.19 | 3.6 | 2.68 | 2.72 | 2.19 | 2.19 | 39.08 | 45.87 | 35.36 | 41.15 | 0.82 | 0.8 |
ADBPB | 25.11 | 3.56 | 12.34 | 14.96 | 9.59 | 10.17 | 13.99 | 22.22 | 12.33 | 18.32 | 0.78 | 0.68 |
NPMS | 9.67 | 7.94 | 3.85 | 2.44 | 2.98 | 1.88 | 20.29 | 14.9 | 17.84 | 13.09 | 0.77 | 0.77 |
NPB | 3.12 | 3.03 | 0.17 | 0.23 | 0.13 | 0.19 | 13.18 | 13.41 | 11.52 | 12.25 | 0.76 | 0.84 |
NPPPB | 3.11 | 1.39 | 0.67 | 0.81 | 0.51 | 0.52 | 26.38 | 29.55 | 22.9 | 23.77 | 0.75 | 0.65 |
PBL | 0.21 | 1.27 | 0 | 0 | 0 | 0 | 11.77 | 17.57 | 10.18 | 13.96 | 0.75 | 0.63 |
TNS | 62.05 | 3.56 | 191.54 | 140.03 | 142.42 | 104.68 | 22.3 | 23.11 | 19.23 | 19.98 | 0.74 | 0.75 |
NSPB | 26.83 | 0.41 | 72.78 | 77.2 | 52.66 | 51.89 | 31.8 | 37.68 | 27.05 | 30.89 | 0.72 | 0.67 |
NPPB | 10.09 | 0.18 | 8.17 | 13.53 | 5.77 | 10.18 | 28.32 | 33.64 | 23.8 | 29.18 | 0.71 | 0.75 |
TNP | 21.62 | 64.89 | 22.19 | 20.2 | 15.86 | 15.97 | 21.79 | 22.64 | 18.42 | 20.13 | 0.71 | 0.79 |
PLMS | 6.96 | 9.46 | 0.25 | 7.88 | 0.17 | 7.87 | 7.17 | 29.04 | 5.93 | 29.65 | 0.68 | 1 |
RBLWSMS | 1.28 | 19.85 | 0 | 0 | 0 | 0 | 2.66 | 4.81 | 2.13 | 0 | 0.64 | 0.45 |
SWMS | 0.75 | 160.41 | 0 | 0.38 | 0 | 0.36 | 7.29 | 8.1 | 5.48 | 7.88 | 0.57 | 0.95 |
RBLWPMS | 4.46 | 141.02 | 0.06 | 0.09 | 0.03 | 0.08 | 5.6 | 6.61 | 4.06 | 6.13 | 0.53 | 0.86 |
TNSPP | 2.98 | 10.48 | 0.07 | 0.09 | 0.04 | 0.08 | 9.1 | 11.59 | 6.55 | 10.5 | 0.52 | 0.82 |
NSPPB | 2.74 | 4.64 | 0.18 | 6.04 | 0.08 | 2.37 | 15.5 | 30.97 | 10.04 | 19.41 | 0.42 | 0.39 |
NSPMS | 3.48 | 1.52 | 0.21 | 0.2 | 0 | 0.14 | 13.28 | 14.87 | 0.67 | 12.17 | 0 | 0.67 |
Primer | Bands | PB | MB | PB (%) | MB (%) | PIC | EMR | RP | MI |
---|---|---|---|---|---|---|---|---|---|
HVH(TG)7 | 8 | 4 | 4 | 50 | 50 | 0.23 | 2 | 13.58 | 0.46 |
GA8YT | 6 | 1 | 5 | 16.66 | 83.33 | 0.71 | 0.16 | 5 | 0.11 |
AG8YT | 6 | 1 | 5 | 16.66 | 83.33 | 0.72 | 0.16 | 4.58 | 0.12 |
GT8YC | 4 | 3 | 1 | 75 | 25 | 0.24 | 2.25 | 6.42 | 0.54 |
AG8YC | 5 | 0 | 5 | 0 | 100 | 0.58 | 0 | 6 | 0.00 |
AG8YG | 8 | 2 | 6 | 25 | 75 | 0.48 | 0.5 | 10.33 | 0.24 |
Total | 37 | 11 | 26 | ||||||
Minimum | 4 | 0 | 1 | 0 | 25 | 0.23 | 0 | 4.58 | 0 |
Maximum | 8 | 4 | 6 | 50 | 100 | 0.72 | 2.25 | 13.58 | 0.54 |
Mean | 6.16 | 1.83 | 4.33 | 30.55 | 69.44 | 0.49 | 0.85 | 7.65 | 0.24 |
Accession | Genome Size (Mbp) | H.G. 2 | |
---|---|---|---|
Average | StDev 1 | ||
SBP | 1897.3 | 18.4 | a |
XM1-39 | 1907.3 | 17.0 | a |
JKI-L378 | 1938.0 | 49.0 | ab |
Prt-79 | 1957.4 | 16.2 | ab |
JKI-L377 | 1961.4 | 16.3 | ab |
Mutal | 1967.6 | 121.6 | abc |
JKI-L295 | 1969.0 | 11.8 | abc |
JKI-L210 | 1973.6 | 26.9 | bcd |
LM13 | 1975.7 | 118.4 | bcd |
JKI-L309 | 1979.7 | 37.6 | bcd |
LM231 | 1984.1 | 100.4 | cd |
LM18 | 1986.4 | 54.6 | cde |
XM5 | 2009.1 | 20.1 | cde |
P-20993 | 2021.5 | 22.8 | cde |
Potosi-ISA | 2024.3 | 36.1 | cde |
Potosi-ALE | 2024.8 | 19.3 | cde |
LM27 | 2027.7 | 23.9 | cde |
LM32 | 2040.9 | 17.9 | de |
CM157 | 2040.9 | 43.8 | de |
I82 | 2041.6 | 10.9 | de |
Inti | 2058.1 | 23.9 | ef |
LM268 | 2078.9 | 10.1 | f |
LM81 | 2080.2 | 13.1 | f |
LM34 | 2083.2 | 17.3 | f |
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Guilengue, N.; Alves, S.; Talhinhas, P.; Neves-Martins, J. Genetic and Genomic Diversity in a Tarwi (Lupinus mutabilis Sweet) Germplasm Collection and Adaptability to Mediterranean Climate Conditions. Agronomy 2020, 10, 21. https://doi.org/10.3390/agronomy10010021
Guilengue N, Alves S, Talhinhas P, Neves-Martins J. Genetic and Genomic Diversity in a Tarwi (Lupinus mutabilis Sweet) Germplasm Collection and Adaptability to Mediterranean Climate Conditions. Agronomy. 2020; 10(1):21. https://doi.org/10.3390/agronomy10010021
Chicago/Turabian StyleGuilengue, Norberto, Sofia Alves, Pedro Talhinhas, and João Neves-Martins. 2020. "Genetic and Genomic Diversity in a Tarwi (Lupinus mutabilis Sweet) Germplasm Collection and Adaptability to Mediterranean Climate Conditions" Agronomy 10, no. 1: 21. https://doi.org/10.3390/agronomy10010021
APA StyleGuilengue, N., Alves, S., Talhinhas, P., & Neves-Martins, J. (2020). Genetic and Genomic Diversity in a Tarwi (Lupinus mutabilis Sweet) Germplasm Collection and Adaptability to Mediterranean Climate Conditions. Agronomy, 10(1), 21. https://doi.org/10.3390/agronomy10010021