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The mosaic genome of indigenous African cattle as a unique genetic resource for African pastoralism

a central role in human the genetic history of its success unknown. Here, through whole-genome sequence analysis of 172 indigenous African cattle from 16 breeds representative of the main cattle groups, we identify a major taurine x indicine cattle admixture event dated to c. years ago, which has shaped the genome of today’s cattle in the Horn of Africa. We identify 16 loci linked to African environmental adaptations across crossbred animals showing an excess of taurine or indicine ancestry. These include immune, heat tolerance and reproduction-related genes. Moreover, we identify one highly divergent locus in African taurine cattle, which is putatively linked to trypanotolerance and present in crossbred cattle living in trypanosomosis infested areas. Our findings indicate that a combination of past taurine and recent indicine admixture-derived genetic resources is at the root of the present success of African pastoralism. taurine x indicine taurine and indicine selection across the genome is at the root the success of African cattle pastoralism. These findings are far-reaching in today’s context of improving livestock productivity to respond to the needs of the growing human populations, with further crossbreeding of indigenous African cattle with exotic cattle recommended as one of the pathways for the continent’s food security. A complete characterization at the genome level of African cattle unique adaptations will open the door to sustainable crossbreeding programs combining local environmental adaptation and increased exotic productivity.

. Additionally, we analyzed our data using MALDER 46 to assess the 169 possibility of multiple admixture events. After fitting a single-pulse model, MALDER 170 analysis did not add a new admixture event with enough significance. Also, the lower 171 significance (Z-score) and larger standard errors of the double-pulse model fitting compared 172 to the single-pulse model fitting support the single-pulse admixture model for our data (Fig.   173 3d). When we combined AFH populations excluding Ankole, Kenya Boran, Mursi, and 174 Sheko, we obtained a similar result (Supplementary Table 8). 175 Only the Kenya Boran has a different timing of admixture among the AFH populations, 176 with a very recent admixture signal and similar significances for both the single-and double-177 pulse model fittings (Fig. 3d). It supports recent and ancient admixture signals in Kenya 178 Boran (Extended Data Fig. 6). The Kenya Boran originates from the Ethiopian Boran 47,48 . 179 After they migrated from Ethiopia to Kenya, they underwent selection and improvement with 180 European taurine in the early 20 th century 47,48 . These recent crossbreeding events most likely 181 correspond to the admixture signal (12.77 ± 12.96 generations ago) of the Kenya Boran 182 (Extended Data Fig. 6). We also detect an ancient admixture signal (132.28 ± 13.60 183 generations ago) in the Sheko. 184 In N'Dama, we detected only a recent admixture signal (21.36 ± 2.50 generations ago) 185 (Supplementary Table 7). Previous studies have shown that the N'Dama is composed of 186 several subpopulations with varying degree of indicine ancestry 5,24,49 . The N'Dama 187 population here is from The Gambia, where an indicine ancestry has previously been 188 documented 5,24,49 . Our results now provide a timescale for this recent admixture event. 189 We also performed GLOBETROTTER 50 analysis, based on haplotype-sharing, as an alternative method to estimate admixture time. The 14 African cattle populations, excluding 191 Muturu and N'Dama, show robust evidence of admixture (bootstrap P < 0.01) 192 (Supplementary Table 9). In addition, admixture time estimates from the populations with 193 best-guess model "one-date" range from 94.85 to 158.08 generations ago, in agreement with 194 the results from ALDER (Fig. 3e). The exceptions are the Kenya Boran and Kenana, with 195 best-guess model "multiple-dates" (Supplementary Table 9). crossbreeds, a haplotype of either taurine or indicine ancestry may confer a relative adaptive 201 advantage following selection pressures. Accordingly, such haplotype will be selected in the 202 admixed African cattle population over time. 203 We employed two approaches to identify such loci and haplotypes. We first explored 204 ongoing selective sweep using the integrated haplotype score (iHS). Taking the top 1% 205 windows in terms of the proportion of SNPs with |iHS| ≥ 2 (≥ 60.00%), we obtained a total of  Figs. 8 and 9). Also, the average taurine ancestry of the windows 212 is outside the empirical distribution generated by resampling (Extended Data Fig. 10). This indicates that the overall ancestry of these selected loci is more skewed toward indicine than 214 the whole genome. 215 We then inferred local ancestry across the genome using LOTER 51 and selected the top 216 0.5% windows with the highest taurine or indicine ancestry (Extended Data Fig. 7b). Of  The longest region, 600 kb in length, is observed at BTA7 (Table 1) commonly observed between AFH and AAI than AFH and EAT (Fig. 4) as well as extended haplotypes sharing between EAT and AFH (Fig. 5). This region overlaps 245 with seven protein-coding genes ( Table 1)   To identify such loci, we performed PBS analysis 64 , comparing AFT and EAT using AAI 254 as an outgroup. After filtering out windows with less than 10 SNPs, we remained with 255 1,239,021 autosomal windows (50 kb sliding windows with 2 kb overlapping step). PBS 256 values ranged from -0.1156 to 0.8341, with a mean of 0.0314. After removing windows with 257 AFT (Supplementary Table 11). 260 The strongest PBS signal (0.6740) overlaps with SDK1 on BTA25 (40,052,001-261 40,102,000), approximately 300 kb upstream of CARD11 (Fig. 6). At this region, F st values 262 between AFT and EAT (F st = 0.5173) or AAI (F st = 0.5308) are much higher than the 263 genome-wide level (F st = 0.1106 and F st = 0.1825, respectively) (Fig. 6b). We observe a 264 unique AFT haplotype pattern compared to EAT and AAI, which is present in some AFH 265 breeds (Supplementary Figs. 2 and 3).    The ancestry of the selection signatures in AFH was found to be more skewed toward  Heat tolerance, a characteristic of zebu cattle 73,74 , is a candidate for indicine pre-320 adaptations to climatic challenges. We found two heat shock protein genes (HSPA9 and 321 DNAJC18) at BTA7, which were previously reported as candidate selective loci in African  The identification of an autosomal taurine background in all African cattle leads us to 334 expect a contribution of local taurine ancestry to environmental adaptation and thus its 335 contribution to the success of African cattle pastoralism. One example is the candidate region at BTA11, which overlaps with NLRC4 59 involved in the inflammatory response. It shows 337 extensive haplotype sharing between AFH and taurine (AFT and EAT). Considering the lack 338 of EAT ancestry in AFH cattle, this haplotype likely originates from AFT. Its presence in 339 AFH may have resulted from selection for a better control of the inflammatory response (e.g. anemia and weight loss) and the level of blood parasites 85 . Accordingly, we expect to 345 detect selection signals in some of the humped cattle exposed to trypanosomosis challenges.

346
In our PBS analysis, a selection signature in AFT was found upstream of CARD11,   The authors declare that they have no competing interests.

782
For the calling of the candidate SNPs from the bam files, we created GVCF file using 783 "HaplotypeCaller" in GATK with "-ERC GVCF" option. Individual GVCF files were merged 784 by breeds using "CombineGVCFs" in GATK. We called and selected candidate SNPs from 785 these combined GVCF files using "GenotypeGVCFs" and "SelectVariants", respectively. To 786 avoid possible false-positive calls, we used "VariantFiltration" of GATK as recommended by GATK best practice: (1) SNP clusters were filtered with "--clusterSize 3" and "-- Buffalos. For admixture analysis, we performed LD-based pruning for the genotype data 811 using PLINK v1.9 114 with "--indep-pairwise 50 10 0.1" option as recommended by the 812 developer. Admixture v1.3.0 44 was run increasing K from 1 to 10, where K is the assumed 813 number of ancestral populations. The Delta K method was used to choose the optimal K 115 .

814
Genetic distances between cattle breeds were estimated with the F st estimator as described in 815 Weir and Cockerham 116 using PLINK v1.9 114 .      In addition, we used GLOBETROTTER 50 on 14 African cattle populations (AFH) to 876 estimate haplotype sharing-based admixture time. The GLOBETROTTER method uses a coancestry curve, in which a measure of how often pairs of haplotypes separated by a genetic 878 distance X come from each respective source populations is plotted as a function of the 879 genetic distance X 50 . Given a single admixture event, haplotypes inherited from each source 880 populations theoretically have an exponential size distribution, which leads to an exponential 881 decay of the coancestry curve 50 . GLOBETROTTER fits this curve, allowing us to estimate 882 the rate of the exponential decay, which is an estimate of the admixture time 50 . 883 We specified the 14 African humped cattle populations and the other non-African cattle 884 populations as target and donor populations, respectively. This specification indicates that 885 target haplotypes are allowed to be copied from the donor haplotypes, not from the other 886 target haplotypes. This is recommended when a similar admixture history is shared across the 887 target populations 50 .

888
To reduce the computational load, we performed LD-based pruning for the phased data