Potential Uses of Wild Germplasms of Grain Legumes for Crop Improvement
Abstract
:1. Introduction
2. A Brief History of the Domestication of Major Grain Legumes
3. Plant Domestication: More Than a Syndrome
4. Revisiting the Genetic Diversities and Potentials of Wild Relatives of Crop Plants
5. Traditional and Sequencing-Based Genetic Map** Using Wild Relatives
6. Use of Genetic Diversity in Wild Relatives to Improve Grain Legume Performance
7. Conclusions and Perspectives
Acknowledgments
Author Contributions
Conflicts of Interest
Abbreviations
QTL | Quantitative trait locus |
InDel | Insertion/deletion |
CNV | Copy number variation |
PAV | Present/absent variation |
cM | Centimorgan |
A-BC | Advanced backcross population |
RIL | Recombinant inbred line |
NIL | Near-isogenic line |
NAM | Nested association map** |
MAGIC | Multi-parent advanced generation inter-cross |
LD | Linkage disequilibrium |
GWAS | Genome-wide association studies |
SNP | Single nucleotide polymorphism |
DArT | Diversity Arrays Technology |
RAD | Restriction site-associated DNA marker |
RRL | Reduced-representation library |
CRoPS | Complexity reduction of polymorphic sequence |
GBS | Genoty**-by-sequencing |
IBL | Inbred backcross line |
MATE | Multidrug and toxic compound extrusion |
SRAP | Sequence-related amplified polymorphism |
TRAP | Target region amplification polymorphism |
SRR | Simple sequence repeat |
RAPD | Random amplified polymorphic DNA |
AFLP | Amplified fragment length polymorphism |
Appendix A
Gene | A DNA sequence that determines the appearance of hereditary characteristics in living organisms |
Allele | Each alternative form of a gene, occupying the same position in each pair of homologous chromosomes |
Fst (fixation index) | Measure of population differentiation due to the genetic structure |
Phenotype | A set of inherited characteristics that is dependent on both the genes and the environment |
Genotype | A set of genes that are characteristic of each organism or individual |
QTL (quantitative trait locus) | A locus on the chromosome that is associated with the quantitative variation of a trait |
Association map** | A germplasm-based approach to characterize QTLs or variations by exploiting the historic linkage disequilibrium to associate phenotypes with the underlying genotypes |
Joint-linkage association map** | A family-based approach to characterize QTLs or variations that are shared across families. It differs in power and scope from the characterization of QTLs based on bi-parental populations. |
Marker-assisted selection | A set of tools that use gene markers to select, in a precise manner, the plants with the genetic potential to produce the desired trait for breeding |
Genomics-assisted breeding | A set of genomics tools (using high-throughput approaches) to select in a targeted manner the plants with the genetic potential to produce the desired trait for breeding |
Introgression | The gene flow from one genetic background (individual) to another gene pool (individual) by backcrossing with one of its parent |
Backcross | Crossing of offspring lines with one of the original parental line |
Linkage drag | Offspring with undesirable genetic background inherited from one of the parental lines |
SNP (Single Nucleotide Polymorphism) | Single-nucleotide variations on the DNA sequence within a population or between paired chromosomes |
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Crop | Genus | Species | Germplasm | Assembled Genome Size (Mb) | Predicted Genome Size (Mb) | Available Database(s) * | Reference |
---|---|---|---|---|---|---|---|
Soybean | Glycine | max | Cultivated (William 82) | 950 | 1115 | 1, 2 | [65] |
Soybean | Glycine | soja | Wild | 868 | 1170 | [66] | |
Soybean | Glycine | soja | Wild | 813–985 | 889–1118 | [67] | |
Peanut | Arachis | duranensis | Wild | 1211 | 1250 | 3 | [28] |
Peanut | Arachis | ipaensis | Wild | 1512 | 1560 | [28] | |
Pea | Pisum | sativum | N/D | N/D | 4685 # | 4, 5 | [13] |
Chickpea | Cicer | arietinum | Cultivated (desi-type) | 520 | 740 | 6, 4, 7 | [68] |
Chickpea | Cicer | arietinum | Cultivated (kabuli-type) | 532 | 738 | [69] | |
Chickpea | Cicer | arietinum | Cultivated (desi-type) | 511 | 740 | [70] | |
Chickpea | Cicer | reticulatum | Wild | 416 | 817 | [71] | |
Common bean | Phaseolus | vulgaris | Landrace | 473 | 587 | 6, 4, 8, 2 | [41] |
Common bean | Phaseolus | vulgaris | Breeding lines | 550 | 587 | [72] | |
Lentil | Lens | culinaris | N/D | N/D | 4032 # | 4 | [13] |
Cowpea | Vigna | unguiculata | Cultivated (IT97K-499-35) | Not complete | 620 | 9 | [73] |
Lupin | Lupinus | angustifolius | Cultivated (Tanjil) | 609 | 951 | 6, 10, 11 | [74] |
Lupin | Lupinus | angustifolius | Cultivated (Tanjil) | 598 | 1153 | [75] | |
Pigeonpea | Cajanus | cajan | Cultivated (Asha) | 606 | 833 | 6 | [76] |
Pigeonpea | Cajanus | cajan | Cultivated (Asha) | 511 | 858 | [77] |
Grain Legume | Trait/s | Population Strategy | Genoty**/Map** Strategy | QTL/Gene | Reference |
---|---|---|---|---|---|
Soybean | Salt tolerance, seed anthocyanin content, pod and seed number per plant, growth period, seed coat color, pod color, trailing growth, leaf length/width ratio, nodule number per plant with cultivated incompatible rhizobia strain | RILs (cultivated × wild) | GBS-WGR | CHX cation anti-transporter for salt tolerance, QTLs for the others traits | [66] |
Soybean | Nodule fresh weight per plant, root fresh weight, total plant fresh weight and ureides (μmol per plant) | RILs (cultivated × wild) | GBS-WGR | QTLs | [124] |
Soybean | Antioxidants, phenolics, and flavonoids in seeds | RILs (cultivated × wild) | GBS-WGR | MATE transporters | [9] |
Soybean | Sclerotinia stem rot resistance | 101 lines | GBS-association map** | QTL | [122] |
Soybean | Root traits (tap root length and lateral root number) and shoot length | BC2F5 (cultivated × wild) | SSR and SNP markers | QTLs | [123] |
Soybean | Oil content, flower color, seed coat color, pubescence form and reported domestication-related QTLs | 302 wild and cultivated accessions | GBS-association map** | GWAS signals associated | [80] |
Soybean | Yield, height and maturity | BC2F4 (cultivated × wild) | SSR markers | QTLs | [134] |
Soybean | Soybean cyst nematode resistance | RILs (cultivated × wild) | SSR markers | QTLs | [135] |
Soybean | Soybean cyst nematode resistance | 235 wild soybean accessions | GBS-GWAS | QTLs | [136] |
Common bean | White mold resistance | NILs source of resistance from Andean genotype Jatu Rong | InDel, SCAR, SNP and phaseolin markers | QTLs | [126] |
Common bean | Seed weight, seed size, days to flowering, yield, plant height | BC2F3:5 (cultivated × wild) | Microsatellite, SCAR, and phaseolin markers | QTLs | [127] |
Common bean | White mold resistance | BC2F3 (cultivated × wild) BC1F4:5 (landrace × cultivated) | SSR, SRAP, TRAP markers | QLTs | [125] |
Common bean | Seed weight, seed mineral accumulation: iron concentration (ppm), zinc concentration (ppm), iron content (mg/seed), zinc content (mg/seed) | BC2F3:5 (cultivated × wild) | Microsatellite markers | QTLs | [128] and cited herein |
Chickpea | Seed coat color | Germplasm collection (93 cultivated desi and kabuli and 79 wild) and RILs (landrace × landrace) | GBS-WGR-association and QTL map** | MATE transporter | [137] |
Chickpea | Flowering time | Germplasm collection (92 cultivated desi and kabuli including beaded, landraces and wild) | Genome-wide GBS- and candidate gene-based genoty** | Eight potential known/candidate flowering time-regulating genes and QTLs | [138] |
Chickpea | 100-seed weight, pod and branch number/plant and plant hairiness | RILs (cultivated × wild) | SSR and SNP polymorphism marker-based | QTLs and seed weight regulating ABI3VP1 transcription factor | [139] |
Chickpea | Pod number and seed yield per plant | Two F5 map** populations (cultivated × wild) | GBS-WGR SNP InDel markers | QTLs | [140,141] |
Chickpea | 100-seed weight | RILs (cultivated × landrace) | GBS-WGR | QTLs | [137] |
Peanut | Root-knot nematodes resistance, drought-related traits and agronomic/domestication traits | RILs (wild × wild) | SNP markers and integrated consensus map from Shirasawa et al. 2013 [142] | QTLs | [143] |
Peanut | Water availability, flowering precocity, seed and pod number, length and size, and pod maturity | 87 BC3F1 and 55 BC2F2 [cultivated × wild amphidiploid (A. ipaensis × A. duranensis)] | SSR markers | QTLs | [144] |
Peanut | Root-knot nematode resistance | BC4F2 population (cultivated × wilds) | RAPD markers | Resistance associated to markers | [145] |
Peanut | Plant growth habit, height of the main stem, plant spread and flower color | Chromosome segment substitution lines (CSSLs). [wild synthetic allotetraploid (A. ipaensis × A. duranensis) × cultivated] | SSR markers | QTLs | [146] |
Peanut | Late leaf spot resistance | F2 (A. duranensis × A. stenosperma) | Microsatellite, AFLP and legume anchor markers | QTLs | [142] |
Pea | Mycosphaerella pinodes resistance | RILs (cultivated × wild) | RAPD, Sequence-tagged site and expressed sequence tag markers | QTLs | [147] |
Pea | Seed weight, root/shoot ratio, flowering response, pod dehiscence, seed dormancy, plant height, basal branching | Set of five recombinant inbred populations: wild × cultivated F12; cultivated × wild F6; cultivated × primitive BC1F4; primitive × wild F4; cultivated × landrace F5 | Morphological Markers, allozyme variation and RAPD | QTLs and genes | [148] |
Pigeonpea | Cleistogamous line | F2 (cultivated × wild) | N/A | Gene | [149] |
Pigeonpea | High protein | Cultivated × wild | N/A | Traditional breeding (pedigree method) | [150] |
Pigeonpea | Male sterility lines | BCn (cultivated × wild) | N/A | Traditional breeding | [151] |
Pigeonpea | Drought tolerance and pod borer insect resistance | F2 (wild × cultivated) | Single feature polymorphisms (SFPs) | Genes | [152] |
Lentil | Anthracnose resistance, seed yield, biomass, straw yield, seed weight, harvest index, podding ability and stand at maturity | RILs (wild × cultivated) | N/A | N/A potential material for breeding | [153] |
Cowpea | Floral scent compounds, seed size, pod fiber layer thickness, seed weight, time of flower opening, days to flower | RILs (cultivated × wild) | SSR | QTLs | [154,155,156] |
Yardlong bean (Vigna unguiculata ssp. unguiculata cv.-gr. sesquipedalis) | Pod length | BC1F1 (cultivated × wild) | SSR | QTLs | [157] |
Yardlong bean | Domestication related traits | BC1F1 (cultivated × wild) | SSR | QTLs | [158] |
Yardlong bean | Pod tenderness | BC1F1 and F2 (cultivated × wild) | SSR | QTLs | [159] |
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Muñoz, N.; Liu, A.; Kan, L.; Li, M.-W.; Lam, H.-M. Potential Uses of Wild Germplasms of Grain Legumes for Crop Improvement. Int. J. Mol. Sci. 2017, 18, 328. https://doi.org/10.3390/ijms18020328
Muñoz N, Liu A, Kan L, Li M-W, Lam H-M. Potential Uses of Wild Germplasms of Grain Legumes for Crop Improvement. International Journal of Molecular Sciences. 2017; 18(2):328. https://doi.org/10.3390/ijms18020328
Chicago/Turabian StyleMuñoz, Nacira, Ailin Liu, Leo Kan, Man-Wah Li, and Hon-Ming Lam. 2017. "Potential Uses of Wild Germplasms of Grain Legumes for Crop Improvement" International Journal of Molecular Sciences 18, no. 2: 328. https://doi.org/10.3390/ijms18020328