Structure of the diversity - Simple sequence repeat (SSR) markers-based genetic diversity and p

Chapter 4: Simple sequence repeat (SSR) markers-based genetic diversity and population

4.4 Results

4.4.2 Structure of the diversity

The ad hoc statistics ∆K showed a higher likelihood value at K=2, supporting the presence of two genotypic groups or populations (Figure 4.1). The first genotypic group (Gg1) comprised of 173 accessions of O. sativa and 2 accessions O. glaberrima. Individuals of this group shared more than 98% of their genomes in common. The second genotypic group (Gg2) consisted of 86 accessions of O. glaberrima, O. barthii and O. longistaminata, sharing also 98% of common genomes. Five accessions had a membership probability < 0.7% and were assigned into a mixed genotypic group (Gg-NA). The genetic diversity indices for the two groups obtained from the model-based population structure analysis are summarised in Table 4.2 and inferred ancestry values presented in Appendix 4.2. Group 1 had higher average number of alleles, heterogeneity and gene diversity than group 2. The separation of the African rice genotypic group (Gg2) into O.

glabberima subgroup (Gg-glab) and O. barthii subgroup (Gg-barthii) showed that the two groups had a similar PIC, and gene diversity, but differed in other parameters. Additionally, the Ho of RM5, RM11 and RM19 markers were nil in Gg2-barthii. The frequency of the major allele was higher in O. glaberrima and O. barthii, as compared to the O. sativa group Gg1. However, only a few alleles were found to be specific to Gg2 with markers RM19, RM124, RM215, and RM510 and very few to Gg1 with RM510, and RM1227. Thus, the genetic differentiation was mostly associated with relative differences in allelic frequencies.

Genetic distances were computed as dissimilarities based on the simple matching dissimilarity index. Very distant accessions had an index value of 1, whereas closely related accessions had a dissimilarity index = 0.03. The generated matrix was used for factorial analysis and the first two axes explained 31.3% of the total SSR variations among accessions. A plot of Axis-1 (25.0%) and Axis-2 (6.3%) revealed 2 major groups (Figure 4.2) and the pattern of groupings was basically the same as that of the model-based population partition at K=2. Nearly all accessions assigned to a population at K=2 were in the same group in the factorial analysis, with the mixed group being intermediate between the 2 groups. However, there was much more within group variation for accessions that belong to Group 1, as confirmed in a subsequently drawn tree using the Unweighted Neighbour Joining Method (UNJM) (Fig 4.3). This suggests that there was a

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hidden sub-structure in that cluster that was not detected by STRUCTURE. Therefore, population structure analysis was again performed only for accessions from Group 1. The ad hoc statistics

∆K showed a higher likelihood value at K=2, suggesting the presence of two subgroups within Group 1, as shown by the tree derived from UNJM (Figure 4.4). The first sub-group (Gg1-1) consisted of 54.4% of accessions from Gg1 and included floating and photosensitive traditional O. sativa accessions of which reference variety, RAM63, from Mali and two cultivars released in Niger in 1952; a cultivar labelled D5237 (also called "white Degaulle" as opposite to "red Degaulle", both named after the former French president the General Charles De Gaulle, because of his tall height) and in 1959, a cultivar called "Santane Diofor"; also clustered into that group.

Cultivar D5237 is a deepwater variety, whereas Satane Diofor is a very plastic variety, which can adapt to various hydrological conditions. The second sub-group (Gg1-2) included accessions collected from the irrigated and rainfed lowland ecosystems. The irrigated control varieties IR64, B6144, as well as the upland Moroberekan, the interspecific NERICA7 and Nipponbare are also in this subgroup.

Twelve accessions, were too admixed to be assigned to any of the two genetically distinct sub- populations of Gg1, and were assigned into a mixed group (Gg1-NA). These 12 accessions shared 49% and 51% of genome of Gg1-1 and Gg1-2, respectively. They were essentially irrigated rice accessions, of which the aromatic reference variety Basmati 370. Accessions like

"Gambiaka" and "Taiwan" already designated by farmers as "perfumed varieties" clustered also into this subgroup. These 12 accessions shared, 49% and 51% of genome of Gg1-1 and Gg1-2, respectively. However, they were scattered within the ecological groups observed in the genetic tree, without any clear relationship (Figure 4.4).

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Table 4.2: Genetic diversity among the two groups composed by individuals sharing more than 70% ancestry in Niger, and genetic diversity among the two species within Gg2 assessed at 18 SSR loci

Marker Gg1 (N = 173) Gg2 (N = 86) Gg2-glab. (N = 60) Gg2-barthii (N = 25)

Na maF D Ho PIC Na maF D Ho PIC Na maF D Ho PIC Na maF D Ho PIC RM1 14.0 0.36 0.79 0.20 0.77 8.0 0.89 0.21 0.07 0.21 8.0 0.91 0.18 0.07 0.17 5.0 0.83 0.30 0.08 0.28 RM5 8.0 0.50 0.64 0.15 0.58 3.0 0.92 0.14 0.05 0.13 3.0 0.94 0.11 0.07 0.11 2.0 0.88 0.21 0.00 0.19 RM11 9.0 0.38 0.75 0.12 0.72 3.0 0.57 0.52 0.05 0.42 3.0 0.51 0.54 0.07 0.43 3.0 0.71 0.43 0.00 0.37 RM19 11.0 0.26 0.80 0.18 0.77 5.0 0.96 0.07 0.05 0.07 5.0 0.95 0.10 0.07 0.10 1.0 1.00 0.00 0.00 0.00 RM25 17.0 0.20 0.90 0.25 0.90 11.0 0.42 0.76 0.20 0.74 10.0 0.38 0.77 0.24 0.75 8.0 0.54 0.67 0.13 0.65 RM44 7.0 0.68 0.49 0.12 0.46 4.0 0.92 0.16 0.02 0.15 4.0 0.92 0.14 0.02 0.14 3.0 0.89 0.20 0.04 0.19 RM124 4.0 0.73 0.43 0.15 0.38 4.0 0.95 0.10 0.03 0.10 3.0 0.95 0.10 0.03 0.09 3.0 0.94 0.11 0.04 0.11 RM154 11.0 0.25 0.83 0.18 0.81 7.0 0.82 0.32 0.11 0.31 5.0 0.81 0.32 0.07 0.31 6.0 0.82 0.32 0.20 0.31 RM215 7.0 0.37 0.74 0.12 0.71 5.0 0.95 0.10 0.03 0.10 4.0 0.97 0.07 0.03 0.06 3.0 0.90 0.18 0.04 0.17 RM237 5.0 0.52 0.61 0.08 0.54 6.0 0.78 0.37 0.11 0.35 5.0 0.82 0.31 0.12 0.29 5.0 0.67 0.52 0.08 0.49 RM271 9.0 0.36 0.69 0.16 0.63 8.0 0.39 0.73 0.16 0.68 8.0 0.40 0.73 0.19 0.69 6.0 0.40 0.70 0.12 0.65 RM287 10.0 0.26 0.82 0.31 0.79 9.0 0.48 0.58 0.23 0.49 6.0 0.52 0.56 0.22 0.47 6.0 0.52 0.60 0.28 0.52 RM316 5.0 0.78 0.37 0.10 0.34 4.0 0.76 0.39 0.08 0.36 4.0 0.72 0.45 0.10 0.40 4.0 0.86 0.25 0.04 0.24 RM431 7.0 0.52 0.62 0.13 0.56 4.0 0.66 0.49 0.12 0.42 4.0 0.68 0.48 0.13 0.42 3.0 0.60 0.51 0.08 0.41 RM447 7.0 0.55 0.62 0.20 0.57 4.0 0.50 0.55 0.21 0.45 3.0 0.57 0.52 0.20 0.42 4.0 0.54 0.57 0.24 0.49 RM510 5.0 0.86 0.26 0.07 0.25 2.0 0.94 0.11 0.07 0.10 2.0 0.92 0.14 0.08 0.13 2.0 0.98 0.04 0.04 0.04 RM1227 7.0 0.73 0.41 0.10 0.36 6.0 0.80 0.35 0.15 0.34 6.0 0.81 0.34 0.18 0.32 5.0 0.78 0.38 0.04 0.36 RM14643 9.0 0.70 0.49 0.06 0.47 6.0 0.89 0.20 0.10 0.20 6.0 0.88 0.23 0.12 0.22 4.0 0.92 0.15 0.08 0.15

152 99.0 89 73

8.44 0.50 0.63 0.15 0.59 5.50 0.76 0.34 0.10 0.31 4.94 0.76 0.34 0.11 0.31 4.06 0.77 0.34 0.09 0.31 N : Number of accessions ; maF : major allele frequency; Na : mean number of alleles per locus; D : mean gene diversity rate per locus; Ho : mean heterogeneity rate per locus; PIC : polymorphism Information content; Gg2 (O. glaberrima and O. barthii, the one sample of O. longistaminata was excluded for this estimation)

124 Gg1 (A) Gg2

(B)

Figure 4.1: (A): Ancestries of 272 ric e accessions estimated from 18 SSR loci using Structure.

(B): number of populations detected from computing ΔK

Figure 4.2 : F actorial analysis of c orrespondence of 272 ric e a ccessions displaying two main groups, and admixed plotted on A xis 1 a nd Axis 2. Gg1 (labelled 1 in red), Gg2 (labelled 2 in green) and admixed (labelled NA). Axis 1 (25.01) and 2 (6.29)

0 5 10 15

0 2 4 6 8 10 12

ΔK

Factorial analysis: Axes 1 / 2

-.6 -.5 -.4 -.3 -.2 -.1 .1 .2 .3 .4

.4 .35 .3 .25 .2 .15 .1 .05

-.05 -.1 -.15 -.2 -.25 -.3 -.35 2 2

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Moro IR64

RAM63 B6144

Basmati370 Nipponbare

NERICA 7

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RAM63 B6144

B6144

Basmati370 Nipponbare

NERICA 7

-.2 NA NA

NA NA NA NA

NA NA

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Gg1

Admixed

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Figure 4.3: Unrooted tree of simple matching distances, based on neighbour joining, of 272 rice accessions at 18 SSR loci. The genetic groups detected by STRUCTURE displayed following the ecology (f: floating, i: irr igated a nd L: lowland). For G g1: Floating is labelled in deep blue, Irrigated in green and Lowland in red; For Gg2, O. glaberrima is colored in light blue and O.

barthii in purple

0 0.5

2f 2L

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IR64 RAM63

B6144 Basmati

Nipponbare

NERICA7 1i

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1f1f1f 1f1f 1f1f 1f

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IR64 IR64 RAM63 RAM631f RAM631f RAM63 RAM63

NERICA7

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2f 2f2f 2L2f2f2f2f2f2f2f2f2f2f2f

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CG14 CG14 CG14 CG14

Gg2

Gg1

Admixed

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Figure 4.4: Unrooted tree of simple matching distances, based on neighbour joining, of 180 rice accessions of Gg1 at 18 SSR loci. Ecologies are differentiated by colour and letter: f= Floating is in deep blue, i = Irrigated in green and L= Lowland in red. Admixed genotypes are labelled 1-NA

Dalam dokumen Genetic diversity of Oryza species in Niger ; screening and breeding for resistance to rice yellow mottle virus (RYMV) (Halaman 135-140)